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H2-reduced structure of E. coli hydrogenase-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other structure of as-isolated hydrogenase-1 refined at 1.67 Angstroem resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 PEG4000, LiSO4, DTT, DMM, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.07 40.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.71 α = 90 b = 97.4 β = 90 c = 183.73 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 CCD ADSC QUANTUM 315r Toroidal mirror 2011-09-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.00407 ESRF ID23-1
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 1.47 29.57 99 0.069 10.35 2.647 547509 283897 -3 16.861
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 1.47 1.5 98.9 0.373 2.79
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 structure of as-isolated hydrogenase-1 refined at 1.67 Angstroem resolution 1.47 25 283873 283873 14104 99.84 0.1243 0.1243 0.1224 0.1235 0.16 0.1614 RANDOM 12.7922
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] -0.23 0.33 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.24 r_dihedral_angle_4_deg 15.264 r_dihedral_angle_3_deg 11.887 r_scangle_it 5.671 r_dihedral_angle_1_deg 5.619 r_scbond_it 4.162 r_mcangle_it 2.87 r_rigid_bond_restr 2.204 r_mcbond_it 2.029 r_angle_refined_deg 1.223
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.24 r_dihedral_angle_4_deg 15.264 r_dihedral_angle_3_deg 11.887 r_scangle_it 5.671 r_dihedral_angle_1_deg 5.619 r_scbond_it 4.162 r_mcangle_it 2.87 r_rigid_bond_restr 2.204 r_mcbond_it 2.029 r_angle_refined_deg 1.223 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13182 Nucleic Acid Atoms Solvent Atoms 1606 Heterogen Atoms 132
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction MxCuBE data collection XDS data reduction REFMAC phasing