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The crystal structure of [Fe]-hydrogenase holoenzyme (HMD) from METHANOCALDOCOCCUS JANNASCHII cocrystallized with cyanide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BOJ PDB ENTRY 2BOJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 283 50% MPD, 0.1M TRIS/HCL, 20mM NH4H2PO4, cyanide, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Crystal Properties Matthews coefficient Solvent content 2.64 53.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.14 α = 90 b = 97.14 β = 90 c = 166.03 γ = 90
Symmetry Space Group I 41 2 2
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 MARMOSAIC 225 mm CCD mirrors 2007-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.99198 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.75 30 0.901 0.065 0.065 18.3 6.1 36729 36729
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.8 73.1 0.49 0.51 4 5.2 2389
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 2BOJ 1.75 10 36673 36673 1944 96.31 0.1883 0.1883 0.18653 0.1866 0.22154 0.2204 RANDOM 34.124
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] 0.2 0.2 -0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.785 r_dihedral_angle_4_deg 19.369 r_dihedral_angle_3_deg 14.394 r_dihedral_angle_1_deg 5.372 r_scangle_it 4.057 r_scbond_it 2.613 r_angle_refined_deg 1.722 r_mcangle_it 1.541 r_mcbond_it 1.064 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.785 r_dihedral_angle_4_deg 19.369 r_dihedral_angle_3_deg 14.394 r_dihedral_angle_1_deg 5.372 r_scangle_it 4.057 r_scbond_it 2.613 r_angle_refined_deg 1.722 r_mcangle_it 1.541 r_mcbond_it 1.064 r_nbtor_refined 0.3 r_nbd_refined 0.214 r_chiral_restr 0.21 r_symmetry_vdw_refined 0.183 r_symmetry_hbond_refined 0.16 r_xyhbond_nbd_refined 0.155 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2591 Nucleic Acid Atoms Solvent Atoms 214 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection XDS data reduction XDS data scaling EPMR phasing