HEADER OXYGEN STORAGE 30-NOV-23 8R9G TITLE MULTICOPY-REFINED CARBOXYMYOGLOBIN PHOTOLYSIS TIME SERIES AT 23 MJ/CM2 TITLE 2 LASER FLUENCE, 600 FS TIME DELAY COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYOGLOBIN; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: EQUUS CABALLUS; SOURCE 3 ORGANISM_COMMON: HORSE; SOURCE 4 ORGANISM_TAXID: 9796 KEYWDS FREE-ELECTRON LASER, TIME-RESOLVED CRYSTALLOGRAPHY, SERIAL KEYWDS 2 CRYSTALLOGRAPHY, OXYGEN STORAGE EXPDTA X-RAY DIFFRACTION AUTHOR T.BARENDS,I.SCHLICHTING REVDAT 4 06-MAR-24 8R9G 1 JRNL REVDAT 3 28-FEB-24 8R9G 1 JRNL REVDAT 2 21-FEB-24 8R9G 1 JRNL REVDAT 1 31-JAN-24 8R9G 0 JRNL AUTH T.R.M.BARENDS,A.GOREL,S.BHATTACHARYYA,G.SCHIRO,C.BACELLAR, JRNL AUTH 2 C.CIRELLI,J.P.COLLETIER,L.FOUCAR,M.L.GRUNBEIN,E.HARTMANN, JRNL AUTH 3 M.HILPERT,J.M.HOLTON,P.J.M.JOHNSON,M.KLOOS,G.KNOPP, JRNL AUTH 4 B.MAREKHA,K.NASS,G.NASS KOVACS,D.OZEROV,M.STRICKER,M.WEIK, JRNL AUTH 5 R.B.DOAK,R.L.SHOEMAN,C.J.MILNE,M.HUIX-ROTLLANT,M.CAMMARATA, JRNL AUTH 6 I.SCHLICHTING JRNL TITL INFLUENCE OF PUMP LASER FLUENCE ON ULTRAFAST MYOGLOBIN JRNL TITL 2 STRUCTURAL DYNAMICS. JRNL REF NATURE V. 626 905 2024 JRNL REFN ESSN 1476-4687 JRNL PMID 38355794 JRNL DOI 10.1038/S41586-024-07032-9 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 9.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 25099 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.180 REMARK 3 FREE R VALUE TEST SET COUNT : 1801 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 9.9600 - 3.2500 1.00 1870 142 0.1618 0.2257 REMARK 3 2 3.2500 - 2.5900 1.00 1821 142 0.1883 0.2083 REMARK 3 3 2.5900 - 2.2700 1.00 1808 139 0.1836 0.2116 REMARK 3 4 2.2700 - 2.0600 1.00 1801 137 0.1772 0.2302 REMARK 3 5 2.0600 - 1.9200 1.00 1790 142 0.1845 0.2081 REMARK 3 6 1.9200 - 1.8000 1.00 1797 134 0.1880 0.1884 REMARK 3 7 1.8000 - 1.7100 1.00 1785 138 0.1930 0.2484 REMARK 3 8 1.7100 - 1.6400 1.00 1779 143 0.1995 0.2211 REMARK 3 9 1.6400 - 1.5800 1.00 1801 137 0.1973 0.2570 REMARK 3 10 1.5800 - 1.5200 1.00 1777 137 0.2029 0.2254 REMARK 3 11 1.5200 - 1.4800 1.00 1778 137 0.2213 0.2219 REMARK 3 12 1.4800 - 1.4300 1.00 1762 135 0.2356 0.2476 REMARK 3 13 1.4300 - 1.4000 0.96 1729 138 0.2719 0.2940 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.121 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.936 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.38 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.02 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.010 2560 REMARK 3 ANGLE : 1.182 3468 REMARK 3 CHIRALITY : 0.081 356 REMARK 3 PLANARITY : 0.011 428 REMARK 3 DIHEDRAL : 15.066 942 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8R9G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-DEC-23. REMARK 100 THE DEPOSITION ID IS D_1292134964. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAR-19 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : FREE ELECTRON LASER REMARK 200 BEAMLINE : ESB REMARK 200 X-RAY GENERATOR MODEL : SWISSFEL ARAMIS BEAMLINE ESB REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.03 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI JUNGFRAU 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTFEL 0.8.0 REMARK 200 DATA SCALING SOFTWARE : CRYSTFEL 0.8.0 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25099 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.320 REMARK 200 RESOLUTION RANGE LOW (A) : 10.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 82.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 3.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.32 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.35 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.1 M AMMONIUM SULFATE, BATCH MODE, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 14.40000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 20 72.87 -151.95 REMARK 500 ASP A 20 73.22 -151.66 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 93 NE2 REMARK 620 2 HEM A 201 NA 90.1 REMARK 620 3 HEM A 201 NB 88.7 89.9 REMARK 620 4 HEM A 201 NC 89.5 179.3 89.4 REMARK 620 5 HEM A 201 ND 89.9 89.8 178.6 90.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 93 NE2 REMARK 620 2 HEM A 201 NA 95.5 REMARK 620 3 HEM A 201 NB 95.0 88.7 REMARK 620 4 HEM A 201 NC 95.8 168.5 87.7 REMARK 620 5 HEM A 201 ND 91.4 90.3 173.6 92.0 REMARK 620 N 1 2 3 4 DBREF 8R9G A 1 152 UNP P68082 MYG_HORSE 2 153 SEQRES 1 A 152 GLY LEU SER ASP GLY GLU TRP GLN GLN VAL LEU ASN VAL SEQRES 2 A 152 TRP GLY LYS VAL GLU ALA ASP ILE ALA GLY HIS GLY GLN SEQRES 3 A 152 GLU VAL LEU ILE ARG LEU PHE THR GLY HIS PRO GLU THR SEQRES 4 A 152 LEU GLU LYS PHE ASP LYS PHE LYS HIS LEU LYS THR GLU SEQRES 5 A 152 ALA GLU MET LYS ALA SER GLU ASP LEU LYS LYS HIS GLY SEQRES 6 A 152 THR VAL VAL LEU THR ALA LEU GLY GLY ILE LEU LYS LYS SEQRES 7 A 152 LYS GLY HIS HIS GLU ALA GLU LEU LYS PRO LEU ALA GLN SEQRES 8 A 152 SER HIS ALA THR LYS HIS LYS ILE PRO ILE LYS TYR LEU SEQRES 9 A 152 GLU PHE ILE SER ASP ALA ILE ILE HIS VAL LEU HIS SER SEQRES 10 A 152 LYS HIS PRO GLY ASP PHE GLY ALA ASP ALA GLN GLY ALA SEQRES 11 A 152 MET THR LYS ALA LEU GLU LEU PHE ARG ASN ASP ILE ALA SEQRES 12 A 152 ALA LYS TYR LYS GLU LEU GLY PHE GLN HET HEM A 201 86 HET SO4 A 202 10 HET SO4 A 203 10 HET CMO A 204 4 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM SO4 SULFATE ION HETNAM CMO CARBON MONOXIDE HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 CMO C O FORMUL 6 HOH *112(H2 O) HELIX 1 AA1 SER A 3 ALA A 19 1 17 HELIX 2 AA2 ASP A 20 HIS A 36 1 17 HELIX 3 AA3 PRO A 37 PHE A 43 5 7 HELIX 4 AA4 THR A 51 SER A 58 1 8 HELIX 5 AA5 SER A 58 LYS A 77 1 20 HELIX 6 AA6 HIS A 82 LYS A 96 1 15 HELIX 7 AA7 PRO A 100 HIS A 119 1 20 HELIX 8 AA8 GLY A 124 GLY A 150 1 27 LINK NE2AHIS A 93 FE AHEM A 201 1555 1555 2.11 LINK NE2BHIS A 93 FE BHEM A 201 1555 1555 2.16 CRYST1 64.100 28.800 35.800 90.00 106.90 90.00 P 1 21 1 2 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.015601 0.000000 0.004740 0.00000 SCALE2 0.000000 0.034722 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029194 0.00000 CONECT 1455 2474 CONECT 1456 2475 CONECT 2390 2398 2452 CONECT 2391 2399 2453 CONECT 2392 2404 2418 CONECT 2393 2405 2419 CONECT 2394 2424 2432 CONECT 2395 2425 2433 CONECT 2396 2438 2446 CONECT 2397 2439 2447 CONECT 2398 2390 2400 2466 CONECT 2399 2391 2401 2467 CONECT 2400 2398 2402 2408 CONECT 2401 2399 2403 2409 CONECT 2402 2400 2404 2406 CONECT 2403 2401 2405 2407 CONECT 2404 2392 2402 2466 CONECT 2405 2393 2403 2467 CONECT 2406 2402 CONECT 2407 2403 CONECT 2408 2400 2410 CONECT 2409 2401 2411 CONECT 2410 2408 2412 CONECT 2411 2409 2413 CONECT 2412 2410 2414 2416 CONECT 2413 2411 2415 2417 CONECT 2414 2412 CONECT 2415 2413 CONECT 2416 2412 CONECT 2417 2413 CONECT 2418 2392 2420 2468 CONECT 2419 2393 2421 2469 CONECT 2420 2418 2422 2426 CONECT 2421 2419 2423 2427 CONECT 2422 2420 2424 2428 CONECT 2423 2421 2425 2429 CONECT 2424 2394 2422 2468 CONECT 2425 2395 2423 2469 CONECT 2426 2420 CONECT 2427 2421 CONECT 2428 2422 2430 CONECT 2429 2423 2431 CONECT 2430 2428 CONECT 2431 2429 CONECT 2432 2394 2434 2470 CONECT 2433 2395 2435 2471 CONECT 2434 2432 2436 2440 CONECT 2435 2433 2437 2441 CONECT 2436 2434 2438 2442 CONECT 2437 2435 2439 2443 CONECT 2438 2396 2436 2470 CONECT 2439 2397 2437 2471 CONECT 2440 2434 CONECT 2441 2435 CONECT 2442 2436 2444 CONECT 2443 2437 2445 CONECT 2444 2442 CONECT 2445 2443 CONECT 2446 2396 2448 2472 CONECT 2447 2397 2449 2473 CONECT 2448 2446 2450 2454 CONECT 2449 2447 2451 2455 CONECT 2450 2448 2452 2456 CONECT 2451 2449 2453 2457 CONECT 2452 2390 2450 2472 CONECT 2453 2391 2451 2473 CONECT 2454 2448 CONECT 2455 2449 CONECT 2456 2450 2458 CONECT 2457 2451 2459 CONECT 2458 2456 2460 CONECT 2459 2457 2461 CONECT 2460 2458 2462 2464 CONECT 2461 2459 2463 2465 CONECT 2462 2460 CONECT 2463 2461 CONECT 2464 2460 CONECT 2465 2461 CONECT 2466 2398 2404 2474 CONECT 2467 2399 2405 2475 CONECT 2468 2418 2424 2474 CONECT 2469 2419 2425 2475 CONECT 2470 2432 2438 2474 CONECT 2471 2433 2439 2475 CONECT 2472 2446 2452 2474 CONECT 2473 2447 2453 2475 CONECT 2474 1455 2466 2468 2470 CONECT 2474 2472 CONECT 2475 1456 2467 2469 2471 CONECT 2475 2473 CONECT 2476 2478 2480 2482 2484 CONECT 2477 2479 2481 2483 2485 CONECT 2478 2476 CONECT 2479 2477 CONECT 2480 2476 CONECT 2481 2477 CONECT 2482 2476 CONECT 2483 2477 CONECT 2484 2476 CONECT 2485 2477 CONECT 2486 2488 2490 2492 2494 CONECT 2487 2489 2491 2493 2495 CONECT 2488 2486 CONECT 2489 2487 CONECT 2490 2486 CONECT 2491 2487 CONECT 2492 2486 CONECT 2493 2487 CONECT 2494 2486 CONECT 2495 2487 CONECT 2496 2498 CONECT 2497 2499 CONECT 2498 2496 CONECT 2499 2497 MASTER 239 0 4 8 0 0 0 6 1361 1 114 12 END