☰ Navigation Tabs
Hydrogenase-2 variant R479K - reduced sample exposed to pure oxygen
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EN9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 296 100mM Bis-tris pH 6.5,
200 mM MgCl2,
18-21% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.42 49.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.729 α = 90 b = 101.332 β = 90 c = 170.681 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 2M 2017-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9282 Diamond I04-1
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 1.3 87.133 99.5 0.19 0.21 0.09 0.99 8 10.4 423495
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 1.3 1.32 1.94 2 0.93 0.776 1.5
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6en9 1.3 87.133 423263 20792 99.477 0.147 0.1466 0.1481 0.1627 0.164 13.004
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] 0.268 0.217 -0.485
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.274 r_dihedral_angle_4_deg 20.101 r_dihedral_angle_3_deg 11.802 r_dihedral_angle_1_deg 6.477 r_lrange_it 4.985 r_lrange_other 4.632 r_scangle_it 3.686 r_scangle_other 3.686 r_scbond_it 2.436 r_scbond_other 2.436
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.274 r_dihedral_angle_4_deg 20.101 r_dihedral_angle_3_deg 11.802 r_dihedral_angle_1_deg 6.477 r_lrange_it 4.985 r_lrange_other 4.632 r_scangle_it 3.686 r_scangle_other 3.686 r_scbond_it 2.436 r_scbond_other 2.436 r_angle_refined_deg 1.924 r_mcangle_it 1.724 r_mcangle_other 1.724 r_angle_other_deg 1.5 r_mcbond_it 1.209 r_mcbond_other 1.209 r_symmetry_xyhbond_nbd_refined 0.252 r_nbd_refined 0.22 r_symmetry_nbd_other 0.174 r_nbd_other 0.165 r_xyhbond_nbd_refined 0.162 r_metal_ion_refined 0.162 r_nbtor_refined 0.159 r_symmetry_xyhbond_nbd_other 0.123 r_chiral_restr 0.103 r_symmetry_nbd_refined 0.102 r_symmetry_nbtor_other 0.089 r_symmetry_metal_ion_refined 0.023 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12650 Nucleic Acid Atoms Solvent Atoms 1809 Heterogen Atoms 114
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing