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X-ray structure of the iron-peroxide intermediate of superoxide reductase (E114A mutant) from Desulfoarculus baarsii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VZI PDB ENTRY 1VZI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 293 16 % PEG 4000, 100 MM TRIS/HNO3 PH9.0, 0.2 M CA(NO3)2 AND 25 MG/ML PROTEIN MIXED 1:1, HANGING DROP VAPOUR DIFFUSION, 20C, pH 9.00
Crystal Properties Matthews coefficient Solvent content 2.6 52.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.45 α = 90 b = 82.9 β = 90 c = 202.66 γ = 90
Symmetry Space Group I 2 2 2
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 MIRRORS 2006-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 1.95 47.1 97.8 0.09 10.27 4 42838 -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 1.94 2.06 94.7 0.6 2.09 3.7
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 1VZI 1.95 47.13 42472 2147 98.4 0.217 0.217 0.2188 0.249 0.2477 RANDOM 35.2
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] 1.3 -6.35 5.05
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.8 c_scangle_it 3.07 c_mcangle_it 2.23 c_scbond_it 2.05 c_angle_deg 1.5 c_mcbond_it 1.41 c_improper_angle_d 0.77 c_bond_d 0.007 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.8 c_scangle_it 3.07 c_mcangle_it 2.23 c_scbond_it 2.05 c_angle_deg 1.5 c_mcbond_it 1.41 c_improper_angle_d 0.77 c_bond_d 0.007 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 3899 Nucleic Acid Atoms Solvent Atoms 309 Heterogen Atoms 22
Software Software Software Name Purpose CNS refinement XDS data reduction XDS data scaling PHASER phasing