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Crystal structure at 1.5 A resolution of an H2-reduced, O2-tolerant hydrogenase from Ralstonia eutropha unmasks a novel iron-sulfur cluster
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WUL PDB ENTRY 1WUL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 282 20-30% polyethylene glycol 3350, 100 mM Bis-(2-hydroxy-ethyl)-amino-tris(hydroxymethyl)-methane buffer, pH 5.5-6.5, VAPOR DIFFUSION, SITTING DROP, temperature 282K
Crystal Properties Matthews coefficient Solvent content 1.99 38.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.091 α = 90 b = 95.646 β = 90 c = 119.145 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 mirrors 2010-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.93950 ESRF ID14-4
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 1.5 59.57 100 0.088 0.088 11.2 6 133947 126968 2 2
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 1.5 1.58 100 0.434 0.434 3.7 5.9 19348
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 1WUL 1.5 59.57 126968 126968 6726 99.85 0.14035 0.14035 0.13967 0.166 0.15293 0.1691 RANDOM 23.691
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] -0.07 -0.47 0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.536 r_dihedral_angle_4_deg 16.376 r_dihedral_angle_3_deg 11.299 r_dihedral_angle_1_deg 6.33 r_angle_refined_deg 1.267 r_chiral_restr 0.093 r_bond_refined_d 0.01 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6827 Nucleic Acid Atoms Solvent Atoms 830 Heterogen Atoms 31
Software Software Software Name Purpose MxCuBE data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling