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Crystal structure of an O2-tolerant [NiFe]-hydrogenase from Ralstonia eutropha in its as-isolated form - oxidized state 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RGW PDB ENTRY 3RGW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 283 20-30% PEG3350, 100 mM Bis-Tris methane, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Crystal Properties Matthews coefficient Solvent content 1.97 37.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.903 α = 90 b = 95.39 β = 90 c = 118.818 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 RAYONIX MX-225 mirrors 2010-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.91842 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.61 34.05 100 0.059 0.059 14.9 4.1 107786
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.61 1.7 100 0.475 0.475 2.9 4.1 15580
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1.61 34.05 102094 102094 5374 99.77 0.13009 0.13009 0.12821 0.1383 0.16577 0.1738 RANDOM 16.576
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] -0.01 -0.07 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.468 r_sphericity_free 26.007 r_dihedral_angle_4_deg 16.741 r_dihedral_angle_3_deg 11.139 r_sphericity_bonded 8.434 r_dihedral_angle_1_deg 5.515 r_rigid_bond_restr 2.777 r_angle_refined_deg 1.287 r_chiral_restr 0.076 r_bond_refined_d 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.468 r_sphericity_free 26.007 r_dihedral_angle_4_deg 16.741 r_dihedral_angle_3_deg 11.139 r_sphericity_bonded 8.434 r_dihedral_angle_1_deg 5.515 r_rigid_bond_restr 2.777 r_angle_refined_deg 1.287 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6785 Nucleic Acid Atoms Solvent Atoms 602 Heterogen Atoms 64
Software Software Software Name Purpose MAR345 data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling