HEADER STRUCTURAL PROTEIN 09-SEP-21 7S4R TITLE SERIAL MACROMOLECULAR CRYSTALLOGRAPHY AT ALBA SYNCHROTRON LIGHT SOURCE TITLE 2 - ALPHA SPECTRIN-SH3 DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPECTRIN ALPHA CHAIN, NON-ERYTHROCYTIC 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ALPHA-II SPECTRIN,FODRIN ALPHA CHAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 3 ORGANISM_COMMON: CHICKEN; SOURCE 4 ORGANISM_TAXID: 9031; SOURCE 5 GENE: SPTAN1, SPTA2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS SERIAL CRYSTALLOGRAPHY, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.M.MARTIN-GARCIA,S.BOTHA,H.HU,R.JERNIGAN,A.CASTELLVI,S.LISOVA,F.GIL, AUTHOR 2 B.CALISTO,I.CRESPO,S.ROY-CHOWDBURY,A.GRIECO,G.KETAWALA,U.WEIERSTALL, AUTHOR 3 J.SPENCE,P.FROMME,N.ZATSEPIN,R.BOER,X.CARPENA REVDAT 3 18-OCT-23 7S4R 1 REMARK REVDAT 2 18-MAY-22 7S4R 1 JRNL REVDAT 1 27-OCT-21 7S4R 0 JRNL AUTH J.M.MARTIN-GARCIA,S.BOTHA,H.HU,R.JERNIGAN,A.CASTELLVI, JRNL AUTH 2 S.LISOVA,F.GIL,B.CALISTO,I.CRESPO,S.ROY-CHOWDHURY,A.GRIECO, JRNL AUTH 3 G.KETAWALA,U.WEIERSTALL,J.SPENCE,P.FROMME,N.ZATSEPIN, JRNL AUTH 4 D.R.BOER,X.CARPENA JRNL TITL SERIAL MACROMOLECULAR CRYSTALLOGRAPHY AT ALBA SYNCHROTRON JRNL TITL 2 LIGHT SOURCE. JRNL REF J.SYNCHROTRON RADIAT. V. 29 896 2022 JRNL REFN ESSN 1600-5775 JRNL PMID 35511023 JRNL DOI 10.1107/S1600577522002508 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.64 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 4110 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.900 REMARK 3 FREE R VALUE TEST SET COUNT : 503 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.16 REMARK 3 REFLECTION IN BIN (WORKING SET) : 264 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.13 REMARK 3 BIN R VALUE (WORKING SET) : 0.1741 REMARK 3 BIN FREE R VALUE SET COUNT : 33 REMARK 3 BIN FREE R VALUE : 0.1607 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 463 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 5 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 50.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 62.26 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.56000 REMARK 3 B22 (A**2) : -3.40000 REMARK 3 B33 (A**2) : -0.16000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.195 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.177 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.191 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.696 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.971 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.961 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 472 ; 0.015 ; 0.018 REMARK 3 BOND LENGTHS OTHERS (A): 462 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 639 ; 1.755 ; 1.891 REMARK 3 BOND ANGLES OTHERS (DEGREES): 1066 ; 0.998 ; 2.751 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 55 ; 6.554 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 24 ;43.821 ;24.167 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 90 ;13.862 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 2 ;31.516 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 71 ; 0.093 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 518 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 102 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 223 ; 4.434 ; 5.824 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 222 ; 4.381 ; 5.788 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 277 ; 6.800 ; 8.699 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 278 ; 6.822 ; 8.738 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 249 ; 5.071 ; 6.503 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 246 ; 5.039 ; 6.431 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 361 ; 7.914 ; 9.439 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 494 ;10.911 ;65.330 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 495 ;10.916 ;65.600 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.90 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 3 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 7S4R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-SEP-21. REMARK 100 THE DEPOSITION ID IS D_1000259608. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-SEP-18 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTFEL REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4682 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 42.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 245.0 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.17 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 57.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 4F17 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS WERE OBTAINED BY APPLYING REMARK 280 SEVERAL CONCENTRATION/DILUTION STEPS WITH MILLI-Q WATER INSIDE REMARK 280 STANDARD AMICON ULTRA 0.5 ML CENTRIFUGAL FILTER (3 KDA CUTOFF). REMARK 280 A CRYSTALLINE SLURRY APPEARED WHEN MOST CITRIC ACID BUFFER WAS REMARK 280 REMOVED, EVAPORATION, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 17.10000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 25.40000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.30000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 25.40000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.10000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.30000 REMARK 290 SMTRY3 4 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 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 ASN A 35 119.53 -164.40 REMARK 500 REMARK 500 REMARK: NULL DBREF 7S4R A 7 62 UNP P07751 SPTN1_CHICK 970 1025 SEQRES 1 A 56 GLU LEU VAL LEU ALA LEU TYR ASP TYR GLN GLU LYS SER SEQRES 2 A 56 PRO ARG GLU VAL THR MET LYS LYS GLY ASP ILE LEU THR SEQRES 3 A 56 LEU LEU ASN SER THR ASN LYS ASP TRP TRP LYS VAL GLU SEQRES 4 A 56 VAL ASN ASP ARG GLN GLY PHE VAL PRO ALA ALA TYR VAL SEQRES 5 A 56 LYS LYS LEU ASP FORMUL 2 HOH *5(H2 O) SHEET 1 AA1 5 ARG A 49 PRO A 54 0 SHEET 2 AA1 5 TRP A 41 VAL A 46 -1 N VAL A 44 O GLY A 51 SHEET 3 AA1 5 ILE A 30 ASN A 35 -1 N ASN A 35 O LYS A 43 SHEET 4 AA1 5 LEU A 8 ALA A 11 -1 N VAL A 9 O LEU A 31 SHEET 5 AA1 5 VAL A 58 LYS A 60 -1 O LYS A 59 N LEU A 10 CRYST1 34.200 42.600 50.800 90.00 90.00 90.00 P 21 21 21 4 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 0.029240 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023474 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019685 0.00000