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Threonine to Cysteine (T225C) variant of E coli hydrogenase-1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.9 295 100 mM Bis-tris pH 5.9
200 mM LiSO4
150 mM NaCl
18-21% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.23 44.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.72 α = 90 b = 97.52 β = 90 c = 183.06 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 EIGER X 16M 2019-02-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.979 Diamond I04
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 1.35 86.2 99.6 0.135 0.037 0.999 11.4 12.5 363874
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 1.35 1.37 96 1.54 0.55 0.4 0.9 7.2
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 1.35 86.07 345662 18097 99.53 0.14193 0.14102 0.1489 0.15926 0.1648 RANDOM 13.837
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] 0.14 0.15 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.857 r_dihedral_angle_4_deg 18.223 r_dihedral_angle_3_deg 11.864 r_dihedral_angle_1_deg 6.524 r_long_range_B_refined 4.123 r_long_range_B_other 3.956 r_scangle_other 3.016 r_scbond_other 2.047 r_scbond_it 2.046 r_angle_refined_deg 1.885
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.857 r_dihedral_angle_4_deg 18.223 r_dihedral_angle_3_deg 11.864 r_dihedral_angle_1_deg 6.524 r_long_range_B_refined 4.123 r_long_range_B_other 3.956 r_scangle_other 3.016 r_scbond_other 2.047 r_scbond_it 2.046 r_angle_refined_deg 1.885 r_angle_other_deg 1.64 r_mcangle_it 1.347 r_mcangle_other 1.347 r_mcbond_it 0.967 r_mcbond_other 0.967 r_chiral_restr 0.102 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13160 Nucleic Acid Atoms Solvent Atoms 1520 Heterogen Atoms 114
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing