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E. coli Hydrogenase-2 (hydrogen reduced form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EHQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.7 296 100 mM Bis-tris pH 5.5-5.9,
18-22 % (w/v) PEG 3350,
200 mM MgCl2
Crystal Properties Matthews coefficient Solvent content 2.22 44.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.602 α = 90 b = 100.54 β = 90 c = 168.587 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 2017-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 1.5 168.59 99.2 0.082 0.09 0.039 0.998 10.9 5.4 267144
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 1.5 1.53 98.2 0.954 1.053 0.439 0.714 1.6 5.5
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 6ehq 1.5 86.35 253537 13461 99.07 0.15313 0.15199 0.1544 0.17502 0.1766 RANDOM 19.211
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] 0.8 0.18 -0.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.964 r_dihedral_angle_4_deg 18.55 r_dihedral_angle_3_deg 11.842 r_dihedral_angle_1_deg 6.166 r_long_range_B_refined 4.35 r_long_range_B_other 4.25 r_scangle_other 3.476 r_scbond_it 2.316 r_scbond_other 2.313 r_mcangle_it 1.896
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.964 r_dihedral_angle_4_deg 18.55 r_dihedral_angle_3_deg 11.842 r_dihedral_angle_1_deg 6.166 r_long_range_B_refined 4.35 r_long_range_B_other 4.25 r_scangle_other 3.476 r_scbond_it 2.316 r_scbond_other 2.313 r_mcangle_it 1.896 r_mcangle_other 1.896 r_angle_refined_deg 1.796 r_mcbond_it 1.407 r_mcbond_other 1.407 r_angle_other_deg 1.071 r_chiral_restr 0.118 r_bond_refined_d 0.017 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12640 Nucleic Acid Atoms Solvent Atoms 1113 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing