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Structure of E. coli hydrogenase-1 in complex with cytochrome b
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3UQY PDB ENTRY 3UQY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.9 298 12% PEG4000, 0.1M NaCl, 0.1M NaAc, 0.2M NH4Ac, 0.001M DTT, 0.02% DDM, Tris/HCl, 0.0003M NQNO (a menaquinone analog), pH 5.9, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.4 48.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126 α = 90 b = 165.3 β = 90 c = 212.8 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 PSI PILATUS 6M 2012-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97908 ESRF ID29
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 3.2 49.12 97.8 0.08 11.35 73321 138472 -3 89.561
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 3.2 3.3 97.1 1.054 1.16
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 PDB ENTRY 3UQY 3.3 25 67491 66832 3298 99.27 0.2018 0.2018 0.1999 0.2054 0.236 0.2377 RANDOM 105.957
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] 7.45 -6.89 -0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.949 r_dihedral_angle_3_deg 17.099 r_dihedral_angle_4_deg 15.385 r_dihedral_angle_1_deg 5.28 r_scangle_it 3.834 r_scbond_it 2.306 r_mcangle_it 1.661 r_angle_refined_deg 1.161 r_mcbond_it 0.837 r_chiral_restr 0.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.949 r_dihedral_angle_3_deg 17.099 r_dihedral_angle_4_deg 15.385 r_dihedral_angle_1_deg 5.28 r_scangle_it 3.834 r_scbond_it 2.306 r_mcangle_it 1.661 r_angle_refined_deg 1.161 r_mcbond_it 0.837 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 30002 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms 316
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MxCuBE data collection XDS data reduction