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CRYSTAL STRUCTURE OF THE FREE RADICAL INTERMEDIATE OF PYRUVATE:FERREDOXIN OXIDOREDUCTASE FROM DESULFOVIBRIO AFRICANUS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KEK PDB ENTRY 1KEK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 10% PEG6000, 100MM MGCL2, 100MM NA CACODYLATE PH 6
Crystal Properties Matthews coefficient Solvent content 2.48 48.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.948 α = 90 b = 146.155 β = 90 c = 211.327 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC CCD 2002-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.42 50 97 0.1 11.9 4 101384 3 16.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.42 2.51 94.7 0.29 5.7 3.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1KEK 2.42 47.47 101384 5121 99.1 0.171 0.171 0.1574 0.226 0.2136 RANDOM 24.6
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -5.42 0.02 5.41
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.2 c_scangle_it 5.2 c_scbond_it 3.95 c_mcangle_it 3.32 c_mcbond_it 2.32 c_angle_deg 1.6 c_improper_angle_d 0.94 c_bond_d 0.01 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.2 c_scangle_it 5.2 c_scbond_it 3.95 c_mcangle_it 3.32 c_mcbond_it 2.32 c_angle_deg 1.6 c_improper_angle_d 0.94 c_bond_d 0.01 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18766 Nucleic Acid Atoms Solvent Atoms 964 Heterogen Atoms 116
Software Software Software Name Purpose CNS refinement XDS data reduction XSCALE data scaling CNS phasing