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Hydrogenase-2 variant R479K - As Isolated form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EN9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 296 100 mM Bis Tris pH 6.5, 200 mM MgCl2, 18-22% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.29 46.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.667 α = 90 b = 101.21 β = 90 c = 170.826 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 2M 2017-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9282 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.25 86.8 99.4 0.107 0.122 0.059 0.998 9 8.1 477343
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.25 1.27 91.5 1.64 1.92 0.97 0.553 1.1 7.2
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6en9 1.25 85.559 477111 23819 99.87 0.115 0.1139 0.1154 0.1361 0.1375 14.967
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] 0.441 0.035 -0.476
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.29 r_dihedral_angle_4_deg 19.662 r_dihedral_angle_3_deg 11.687 r_dihedral_angle_1_deg 6.506 r_rigid_bond_restr 5.138 r_scangle_it 3.096 r_scangle_other 3.096 r_lrange_it 2.947 r_lrange_other 2.947 r_scbond_it 2.909
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.29 r_dihedral_angle_4_deg 19.662 r_dihedral_angle_3_deg 11.687 r_dihedral_angle_1_deg 6.506 r_rigid_bond_restr 5.138 r_scangle_it 3.096 r_scangle_other 3.096 r_lrange_it 2.947 r_lrange_other 2.947 r_scbond_it 2.909 r_scbond_other 2.909 r_angle_refined_deg 2.136 r_mcangle_it 1.706 r_mcangle_other 1.706 r_angle_other_deg 1.562 r_mcbond_it 1.549 r_mcbond_other 1.549 r_symmetry_xyhbond_nbd_refined 0.265 r_nbd_refined 0.226 r_nbd_other 0.203 r_symmetry_nbd_other 0.173 r_nbtor_refined 0.16 r_xyhbond_nbd_refined 0.154 r_symmetry_xyhbond_nbd_other 0.144 r_chiral_restr 0.122 r_metal_ion_refined 0.122 r_symmetry_nbtor_other 0.09 r_symmetry_nbd_refined 0.07 r_bond_refined_d 0.019 r_gen_planes_refined 0.013 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12650 Nucleic Acid Atoms Solvent Atoms 1737 Heterogen Atoms 83
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing