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Crystal structure of an O2-tolerant [NiFe]-hydrogenase from Ralstonia eutropha in its as-isolated form - oxidized state 2
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, HANGING DROP 5.5 282 20-30% PEG3350, 100 mM Bis-Tris methane, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 282K
Crystal Properties Matthews coefficient Solvent content 2.03 39.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.618 α = 90 b = 95.742 β = 90 c = 120.702 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 2011-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.91841 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 1.45 34.36 99.7 0.056 0.056 18 5.9 150727 13.52
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 1.45 1.53 98 0.496 0.496 2.7 4.4 21390
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 (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 1.45 34.36 142805 7516 99.42 0.1267 0.1267 0.12509 0.1388 0.15713 0.1642 RANDOM 14.215
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] -0.11 -0.12 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.543 r_sphericity_free 26.357 r_dihedral_angle_4_deg 15.552 r_dihedral_angle_3_deg 11.639 r_sphericity_bonded 7.719 r_dihedral_angle_1_deg 5.917 r_rigid_bond_restr 1.446 r_angle_refined_deg 1.259 r_chiral_restr 0.091 r_bond_refined_d 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.543 r_sphericity_free 26.357 r_dihedral_angle_4_deg 15.552 r_dihedral_angle_3_deg 11.639 r_sphericity_bonded 7.719 r_dihedral_angle_1_deg 5.917 r_rigid_bond_restr 1.446 r_angle_refined_deg 1.259 r_chiral_restr 0.091 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 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 6783 Nucleic Acid Atoms Solvent Atoms 1046 Heterogen Atoms 35
Software Software Software Name Purpose MAR345 data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling