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E. coli Hydrogenase-2 (as isolated form).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5A4M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 100 mM Bis-tris pH 5.5
200 mM MgCl2
18-22% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.19 43.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.064 α = 90 b = 100.09 β = 90 c = 168.135 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 2016-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.976 PETRA III, EMBL c/o DESY P14 (MX2)
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 2.2 86 95.8 0.19 0.12 0.978 6.4 6.5 93703
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 2.2 2.24 95.5 0.98 0.63 0.68 1.7 6.2
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 5A4M 2.2 86 79987 4141 98.46 0.16365 0.16231 0.1698 0.18951 0.1967 RANDOM 29.825
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] 0.95 0.55 -1.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.165 r_dihedral_angle_4_deg 18.612 r_dihedral_angle_3_deg 12.507 r_dihedral_angle_1_deg 5.988 r_long_range_B_refined 3.775 r_long_range_B_other 3.747 r_scangle_other 2.76 r_mcangle_it 1.831 r_mcangle_other 1.831 r_scbond_it 1.667
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.165 r_dihedral_angle_4_deg 18.612 r_dihedral_angle_3_deg 12.507 r_dihedral_angle_1_deg 5.988 r_long_range_B_refined 3.775 r_long_range_B_other 3.747 r_scangle_other 2.76 r_mcangle_it 1.831 r_mcangle_other 1.831 r_scbond_it 1.667 r_scbond_other 1.667 r_angle_refined_deg 1.526 r_mcbond_it 1.137 r_mcbond_other 1.137 r_angle_other_deg 1.01 r_chiral_restr 0.092 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 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 12647 Nucleic Acid Atoms Solvent Atoms 525 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing