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Crystal Structure of the C19G variant of the membrane-bound [NiFe]-Hydrogenase from Cupriavidus necator in the air-oxidized state at 1.61 A Resolution.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RGW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.5 277 20% - 30% PEG3350, 0.1M BIS-TRIS PH 5.5
Crystal Properties Matthews coefficient Solvent content 2.1 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.526 α = 90 b = 95.523 β = 90 c = 118.868 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 PILATUS 6M MIRROR 2013-01-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 46.01 99.9 0.099 1 8.7 5.5 107311
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.61 1.7 100 0.681 0.76 2.3 5.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.61 46.01 101881 5348 99.89 0.13843 0.13713 0.147 0.1632 0.1702 RANDOM 25.173
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 0.17 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.035 r_sphericity_free 27.196 r_dihedral_angle_4_deg 15.994 r_dihedral_angle_3_deg 11.129 r_sphericity_bonded 7.879 r_dihedral_angle_1_deg 5.09 r_long_range_B_refined 2.91 r_long_range_B_other 2.583 r_scangle_other 1.938 r_mcangle_it 1.821
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.035 r_sphericity_free 27.196 r_dihedral_angle_4_deg 15.994 r_dihedral_angle_3_deg 11.129 r_sphericity_bonded 7.879 r_dihedral_angle_1_deg 5.09 r_long_range_B_refined 2.91 r_long_range_B_other 2.583 r_scangle_other 1.938 r_mcangle_it 1.821 r_mcangle_other 1.821 r_rigid_bond_restr 1.757 r_scbond_it 1.638 r_scbond_other 1.636 r_mcbond_it 1.493 r_mcbond_other 1.493 r_angle_refined_deg 1.254 r_angle_other_deg 0.831 r_chiral_restr 0.068 r_bond_refined_d 0.008 r_bond_other_d 0.004 r_gen_planes_refined 0.004 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 6756 Nucleic Acid Atoms Solvent Atoms 597 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing