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Structure of fully reduced variant E28Q of E. coli hydrogenase-1 at pH 8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LMM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.1 296 100 mM tris pH 8.1,
150 mM NaCl,
200 mM LiSO4
19-21 % PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.11 41.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.068 α = 90 b = 97.814 β = 90 c = 183.21 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 PILATUS3 6M 2017-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9686 Diamond I24
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 1.2 94.1 96.6 0.073 0.037 0.998 11.4 5.7 504435
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 1.2 1.22 92.4 0.83 0.46 0.463 1.7 5
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 5LMM 1.2 67.89 478639 25633 96.45 0.11189 0.11077 0.1107 0.13303 0.1327 RANDOM 13.918
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] -0.27 -0.27 0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.712 r_sphericity_free 24.217 r_dihedral_angle_4_deg 17.884 r_dihedral_angle_3_deg 11.929 r_sphericity_bonded 9.503 r_dihedral_angle_1_deg 6.24 r_long_range_B_other 3.061 r_long_range_B_refined 3.06 r_scangle_other 2.394 r_scbond_it 1.992
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.712 r_sphericity_free 24.217 r_dihedral_angle_4_deg 17.884 r_dihedral_angle_3_deg 11.929 r_sphericity_bonded 9.503 r_dihedral_angle_1_deg 6.24 r_long_range_B_other 3.061 r_long_range_B_refined 3.06 r_scangle_other 2.394 r_scbond_it 1.992 r_scbond_other 1.992 r_rigid_bond_restr 1.95 r_angle_refined_deg 1.561 r_mcangle_it 1.45 r_mcangle_other 1.45 r_mcbond_it 1.16 r_mcbond_other 1.16 r_angle_other_deg 0.59 r_chiral_restr 0.088 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13150 Nucleic Acid Atoms Solvent Atoms 1732 Heterogen Atoms 120
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing