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Crystal structure of an O2-tolerant [NiFe]-hydrogenase from Ralstonia eutropha in its as-isolated form with ascorbate - partly reduced state
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 5.5 282 20-30% PEG3350, 100 mM Bis-Tris methane, pH 5.5, crystal soaked in ascorbate, VAPOR DIFFUSION, SITTING DROP, temperature 282K
Crystal Properties Matthews coefficient Solvent content 2.04 39.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.775 α = 90 b = 95.795 β = 90 c = 120.679 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 34.42 99.5 0.061 0.061 17.1 6.3 150757 14.92
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 96.3 0.699 0.699 2.1 4.7 21043
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 34.42 143090 7567 99.4 0.1361 0.1361 0.13457 0.1332 0.16484 0.1618 RANDOM 15.887
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] -0.04 0.03 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.262 r_sphericity_free 24.737 r_dihedral_angle_4_deg 14.679 r_dihedral_angle_3_deg 10.963 r_sphericity_bonded 9.058 r_dihedral_angle_1_deg 5.532 r_rigid_bond_restr 2.843 r_angle_refined_deg 1.367 r_angle_other_deg 1.363 r_chiral_restr 0.074
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.262 r_sphericity_free 24.737 r_dihedral_angle_4_deg 14.679 r_dihedral_angle_3_deg 10.963 r_sphericity_bonded 9.058 r_dihedral_angle_1_deg 5.532 r_rigid_bond_restr 2.843 r_angle_refined_deg 1.367 r_angle_other_deg 1.363 r_chiral_restr 0.074 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.002 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_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 6750 Nucleic Acid Atoms Solvent Atoms 982 Heterogen Atoms 34
Software Software Software Name Purpose MAR345 data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling