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3D structure of the Ni-Fe-Se hydrogenase from D. vulgaris Hildenborough in the as-isolated oxidized state at 1.50 Angstroms
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WPN PDB ENTRY 2WPN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 CRYSTALS WERE GROWN BY THE SITTING DROP VAPOR DIFFUSION METHOD, BY MIXING 1.5 UL OF RESERVOIR SOLUTION CONTAINING 20% POLYETHYLENE GLYCOL (PEG) 1500, 0.1 M TRIS-HCL, PH 8.5 AND AN EQUAL VOLUME OF A SOLUTION COMPOSED OF 10 MG/ML OF PROTEIN IN 10 MM TRIS-HCL BUFFER AT PH 7.6.
Crystal Properties Matthews coefficient Solvent content 2.18 43.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.17 α = 90 b = 97.35 β = 90 c = 102.97 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 MARMOSAIC 225 mm CCD 2009-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA SLS X06DA
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 1.5 45.5 98.6 0.09 17.5 7.2 114933 10.02
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 1.5 1.54 88.5 0.59 3 5.5
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 2WPN 1.5 45.512 0.83 114887 11120 98.61 0.1359 0.1349 0.1325 0.1543 0.1524
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] -1.46 -1.3399 2.7999
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.97 f_angle_d 1.476 f_chiral_restr 0.091 f_bond_d 0.012 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5820 Nucleic Acid Atoms Solvent Atoms 700 Heterogen Atoms 103
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing