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Structure of fully reduced Hydrogenase (Hyd-1) variant E28Q collected at pH 10
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,
200 mm LiSO4
150 mM NaCl
19-21% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.08 40.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.906 α = 90 b = 95.224 β = 90 c = 183.91 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 2017-08-02 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) 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 95 95.9 0.095 8.5 4.7 437084
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.25 1.32 93.1 0.96 1.8
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 1.25 92.12 414972 22000 95.7 0.121 0.12 0.1215 0.147 0.1481 RANDOM 11.36
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] 0.47 -0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.337 r_sphericity_free 19.972 r_dihedral_angle_4_deg 16.557 r_dihedral_angle_3_deg 12.053 r_dihedral_angle_1_deg 6.049 r_sphericity_bonded 5.915 r_rigid_bond_restr 2.593 r_long_range_B_refined 2.334 r_long_range_B_other 2.112 r_scangle_other 2.034
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.337 r_sphericity_free 19.972 r_dihedral_angle_4_deg 16.557 r_dihedral_angle_3_deg 12.053 r_dihedral_angle_1_deg 6.049 r_sphericity_bonded 5.915 r_rigid_bond_restr 2.593 r_long_range_B_refined 2.334 r_long_range_B_other 2.112 r_scangle_other 2.034 r_scbond_it 1.725 r_scbond_other 1.719 r_angle_refined_deg 1.619 r_mcangle_it 1.215 r_mcangle_other 1.215 r_angle_other_deg 1.153 r_mcbond_it 0.988 r_mcbond_other 0.988 r_chiral_restr 0.144 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 13181 Nucleic Acid Atoms Solvent Atoms 1380 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing