☰ Navigation Tabs
Crystal Structure of the C19G/C120G variant of the membrane-bound [NiFe]-Hydrogenase from Cupriavidus necator in the H2-reduced state at 1.92 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 2.02 38.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.201 α = 90 b = 95.506 β = 90 c = 118.978 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 2012-01-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.92 34.2 100 0.091 9.9 4.9 64415
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 1.92 2.02 100 0.531 0.86 2.1 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 1.92 34.2 60918 3245 99.69 0.16826 0.16656 0.174 0.19938 0.2072 RANDOM 29.668
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] -0.24 -1.5 1.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.4 r_sphericity_free 33.096 r_dihedral_angle_4_deg 16.956 r_dihedral_angle_3_deg 12.598 r_sphericity_bonded 6.676 r_dihedral_angle_1_deg 5.52 r_long_range_B_refined 3.458 r_long_range_B_other 3.458 r_mcangle_it 2.063 r_mcangle_other 2.063
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.4 r_sphericity_free 33.096 r_dihedral_angle_4_deg 16.956 r_dihedral_angle_3_deg 12.598 r_sphericity_bonded 6.676 r_dihedral_angle_1_deg 5.52 r_long_range_B_refined 3.458 r_long_range_B_other 3.458 r_mcangle_it 2.063 r_mcangle_other 2.063 r_scangle_other 1.766 r_rigid_bond_restr 1.616 r_mcbond_it 1.581 r_mcbond_other 1.581 r_scbond_it 1.47 r_scbond_other 1.47 r_angle_refined_deg 1.076 r_angle_other_deg 0.768 r_chiral_restr 0.061 r_bond_refined_d 0.007 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 6780 Nucleic Acid Atoms Solvent Atoms 530 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing