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Crystal Structure of the C120G variant of the membrane-bound [NiFe]-Hydrogenase from Cupriavidus necator in the H2-reduced state at 1.65 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 5.5 283 20% - 30% PEG3350, 0.1M BIS-TRIS PH 5.5
Crystal Properties Matthews coefficient Solvent content 2.15 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.415 α = 90 b = 95.751 β = 90 c = 120.597 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-F MIRROR 2013-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.968630 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.65 47.92 98.2 0.99 10.3 5.6 100754
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.74 96.2 0.8 5.6
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 1.65 47.92 95636 5025 97.95 0.1428 0.14125 0.153 0.17195 0.1823 RANDOM 18.53
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] -0.12 -0.56 0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.98 r_sphericity_free 29.443 r_dihedral_angle_4_deg 15.725 r_dihedral_angle_3_deg 11.542 r_sphericity_bonded 6.275 r_dihedral_angle_1_deg 5.388 r_long_range_B_refined 2.972 r_rigid_bond_restr 2.379 r_long_range_B_other 2.156 r_scangle_other 1.265
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.98 r_sphericity_free 29.443 r_dihedral_angle_4_deg 15.725 r_dihedral_angle_3_deg 11.542 r_sphericity_bonded 6.275 r_dihedral_angle_1_deg 5.388 r_long_range_B_refined 2.972 r_rigid_bond_restr 2.379 r_long_range_B_other 2.156 r_scangle_other 1.265 r_angle_refined_deg 1.141 r_mcangle_it 1.133 r_mcangle_other 1.133 r_scbond_it 1.026 r_scbond_other 1.025 r_angle_other_deg 0.848 r_mcbond_it 0.843 r_mcbond_other 0.84 r_chiral_restr 0.065 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.001 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 6809 Nucleic Acid Atoms Solvent Atoms 812 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing