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Stepwise [FeFe]-hydrogenase H-cluster assembly revealed in the structure of HydA(deltaEFG)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FEH PDB entry 1FEH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 capillary batch diffusion 6.5 298 25.5% PEG 8000, 0.085 M sodium cacodylate, 0.17 M sodium acetate trihydrate, 1 mM dithionite, pH 6.5, capillary batch diffusion, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.28 46.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.895 α = 90 b = 70.895 β = 90 c = 155.429 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD ADSC QUANTUM 315r 2008-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.95369 SSRL BL9-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.97 50 97.9 4.4 60782
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.97 2.04 97.2 0.409 2.4 4.2 10553
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 PDB entry 1FEH 1.97 20 57708 3074 97.82 0.173 0.17 0.1714 0.216 0.2187 RANDOM 26.922
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] -1.16 -0.58 -1.16 1.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.182 r_dihedral_angle_4_deg 20.582 r_dihedral_angle_3_deg 13.038 r_scangle_it 9.824 r_scbond_it 7.288 r_mcangle_it 5.056 r_dihedral_angle_1_deg 4.754 r_mcbond_it 4.154 r_angle_refined_deg 0.924 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.182 r_dihedral_angle_4_deg 20.582 r_dihedral_angle_3_deg 13.038 r_scangle_it 9.824 r_scbond_it 7.288 r_mcangle_it 5.056 r_dihedral_angle_1_deg 4.754 r_mcbond_it 4.154 r_angle_refined_deg 0.924 r_nbtor_refined 0.308 r_symmetry_hbond_refined 0.233 r_nbd_refined 0.204 r_xyhbond_nbd_refined 0.196 r_symmetry_vdw_refined 0.128 r_chiral_restr 0.065 r_bond_refined_d 0.006 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6166 Nucleic Acid Atoms Solvent Atoms 775 Heterogen Atoms 26
Software Software Software Name Purpose MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling