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Four-site variant (Y222C, C197S, C432S, C433S) of E. coli hydrogenase-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EQH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.9 296 100 mM bis-tris pH 5.9,
200 mM MgCl2,
19-21 % PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.14 42.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.237 α = 90 b = 100.986 β = 90 c = 169.425 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 2017-09-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9159 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.71 100 100 0.093 0.036 0.999 16.5 7.5 185232
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.71 1.74 100 0.84 0.33 0.819 7.4
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 (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 6EQH 1.71 86.75 176274 8958 99.99 0.15885 0.1573 0.1687 0.18979 0.1971 RANDOM 18.318
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] 0.31 0.42 -0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.402 r_dihedral_angle_4_deg 19.754 r_dihedral_angle_3_deg 11.999 r_dihedral_angle_1_deg 6.116 r_long_range_B_refined 4.192 r_long_range_B_other 4.084 r_scangle_other 3.199 r_scbond_other 2.07 r_scbond_it 2.069 r_mcangle_it 1.837
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.402 r_dihedral_angle_4_deg 19.754 r_dihedral_angle_3_deg 11.999 r_dihedral_angle_1_deg 6.116 r_long_range_B_refined 4.192 r_long_range_B_other 4.084 r_scangle_other 3.199 r_scbond_other 2.07 r_scbond_it 2.069 r_mcangle_it 1.837 r_mcangle_other 1.837 r_angle_refined_deg 1.63 r_mcbond_it 1.267 r_mcbond_other 1.267 r_angle_other_deg 1.047 r_chiral_restr 0.102 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12642 Nucleic Acid Atoms Solvent Atoms 932 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing