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Structure and function of an oxygen tolerant NiFe hydrogenase from Salmonella
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RGW PDB ENTRY 3RGW
Crystallization Crystal Properties Matthews coefficient Solvent content 3.98 69.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.46 α = 90 b = 122.21 β = 95.56 c = 227.82 γ = 90
Symmetry Space Group I 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2012-02-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
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 3.2 29.5 99.6 0.1 9.7 3.8 51795 83.8
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 3.2 3.38 98.6 0.58 1.8 3.8
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 3RGW 3.2 29.52 49122 2639 99.5 0.1605 0.15811 0.1599 0.20467 0.1988 RANDOM 87.343
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] 3.09 -2.73 -1.99 -0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.914 r_dihedral_angle_4_deg 19.165 r_dihedral_angle_3_deg 17.558 r_dihedral_angle_1_deg 6.634 r_mcangle_it 5.268 r_scbond_it 3.723 r_mcbond_it 3.348 r_mcbond_other 3.347 r_angle_refined_deg 1.545 r_angle_other_deg 1.331
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.914 r_dihedral_angle_4_deg 19.165 r_dihedral_angle_3_deg 17.558 r_dihedral_angle_1_deg 6.634 r_mcangle_it 5.268 r_scbond_it 3.723 r_mcbond_it 3.348 r_mcbond_other 3.347 r_angle_refined_deg 1.545 r_angle_other_deg 1.331 r_chiral_restr 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.005 r_gen_planes_other 0.004 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19828 Nucleic Acid Atoms Solvent Atoms 114 Heterogen Atoms 109
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing