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Ethylene glycol inhibited form of Aldehyde oxidoreductase from Desulfovibrio gigas
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VLB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.6 277 isopropanol, MgCl2, pH 7.6, vapor diffusion, sitting drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.45 49.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.8 α = 90 b = 142.8 β = 90 c = 161.55 γ = 120
Symmetry Space Group P 61 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 ADSC QUANTUM 210 2007-09-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 0.931 ESRF ID14-3
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 1.79 29.44 98.4 0.062 0.062 9.421 4.4 89511
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) 1.79 1.89 97.5 0.327 0.327 2.2 3.5 12764
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 1VLB 1.79 29.44 89499 4474 97.93 0.155 0.153 0.1617 0.189 0.1971 RANDOM 19.868
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] -0.02 -0.01 -0.02 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.816 r_dihedral_angle_4_deg 13.652 r_dihedral_angle_3_deg 12.159 r_sphericity_free 10.071 r_dihedral_angle_1_deg 6.357 r_sphericity_bonded 5.179 r_rigid_bond_restr 3.198 r_scangle_it 2.721 r_scbond_it 1.745 r_angle_refined_deg 1.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.816 r_dihedral_angle_4_deg 13.652 r_dihedral_angle_3_deg 12.159 r_sphericity_free 10.071 r_dihedral_angle_1_deg 6.357 r_sphericity_bonded 5.179 r_rigid_bond_restr 3.198 r_scangle_it 2.721 r_scbond_it 1.745 r_angle_refined_deg 1.42 r_mcangle_it 0.972 r_mcbond_it 0.62 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.255 r_nbd_refined 0.2 r_symmetry_hbond_refined 0.177 r_xyhbond_nbd_refined 0.138 r_chiral_restr 0.092 r_bond_refined_d 0.012 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6905 Nucleic Acid Atoms Solvent Atoms 1183 Heterogen Atoms 73
Software Software Software Name Purpose SCALA data scaling PHASER phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction