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Crystal structure of an O2-tolerant [NiFe]-hydrogenase from Ralstonia eutropha in its as-isolated form (oxidized state - state 3)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RGW 3RGW/4IUB experimental model PDB 4IUB 3RGW/4IUB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 277 20-30% PEG3350, 0.1M BIS-TRIS pH 5.5-6.5
Crystal Properties Matthews coefficient Solvent content 2.03 39.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.11 α = 90 b = 95.567 β = 90 c = 119.828 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 PIXEL DECTRIS PILATUS3 6M Mirrors 2016-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.97625 ESRF ID30B
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 1.5 47.78 99.8 0.06 12.4 5.4 134109
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 1.5 1.58 98.9 0.891 1.9 5.2
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 3RGW/4IUB 1.5 47.78 127184 6825 99.71 0.12662 0.1252 0.1252 0.15335 0.1536 RANDOM 25.66
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] -0.05 -0.62 0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.335 r_sphericity_free 20.776 r_dihedral_angle_4_deg 16.057 r_dihedral_angle_3_deg 11.753 r_dihedral_angle_1_deg 5.811 r_sphericity_bonded 5.002 r_long_range_B_refined 2.501 r_long_range_B_other 2.501 r_rigid_bond_restr 1.968 r_scangle_other 1.681
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.335 r_sphericity_free 20.776 r_dihedral_angle_4_deg 16.057 r_dihedral_angle_3_deg 11.753 r_dihedral_angle_1_deg 5.811 r_sphericity_bonded 5.002 r_long_range_B_refined 2.501 r_long_range_B_other 2.501 r_rigid_bond_restr 1.968 r_scangle_other 1.681 r_mcangle_it 1.583 r_mcangle_other 1.583 r_scbond_it 1.454 r_scbond_other 1.451 r_mcbond_it 1.377 r_mcbond_other 1.376 r_angle_refined_deg 1.302 r_angle_other_deg 0.845 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_bond_other_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.001 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6742 Nucleic Acid Atoms Solvent Atoms 652 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing