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V207A Horse Liver Alcohol Dehydrogenase E complexed with NAD and 2,3,4,5,6-pentafluorobenzyl alcohol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DWV PDB ENTRY 4DWV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICRODIALYSIS 7 278 50 mM ammonium n-[tris(hydroxymethyl) methyl]-2-aminoethane sulfonate, pH 6.7 (at 25 C), 0.25 mM EDTA, 10 mg/ml protein, 1 mM NAD+, 10 mM 2,3,4,5,6-pentafluorobenzyl alcohol, 12 TO 25 % 2-methyl-2,4-pentanediol, MICRODIALYSIS, temperature 278K
Crystal Properties Matthews coefficient Solvent content 2.4 48.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.49 α = 91.96 b = 51.23 β = 103 c = 92.32 γ = 110.28
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 NOIR-1 Rosenbaum vertical focussing mirrors 2008-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 0.827 ALS 4.2.2
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 1.2 20 94.2 0.055 11.3 3.77 217807 11.9
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 1.2 1.24 74 0.363 2.4 3.46 17131
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 (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 4DWV 1.2 19.84 216747 1066 94.14 0.13547 0.13547 0.13532 0.1402 0.16569 0.1671 RANDOM 16.966
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] 0.24 -0.49 0.24 0.23 0.15 -0.39
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 41.554 r_dihedral_angle_2_deg 38.114 r_dihedral_angle_4_deg 14.701 r_dihedral_angle_3_deg 11.387 r_sphericity_bonded 10.42 r_dihedral_angle_1_deg 6.244 r_long_range_B_refined 5.096 r_rigid_bond_restr 3.921 r_long_range_B_other 3.814 r_scangle_other 3.088
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 41.554 r_dihedral_angle_2_deg 38.114 r_dihedral_angle_4_deg 14.701 r_dihedral_angle_3_deg 11.387 r_sphericity_bonded 10.42 r_dihedral_angle_1_deg 6.244 r_long_range_B_refined 5.096 r_rigid_bond_restr 3.921 r_long_range_B_other 3.814 r_scangle_other 3.088 r_scbond_it 2.764 r_scbond_other 2.764 r_angle_refined_deg 1.892 r_mcangle_it 1.653 r_mcangle_other 1.653 r_mcbond_it 1.443 r_mcbond_other 1.443 r_angle_other_deg 0.911 r_chiral_restr 0.11 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5566 Nucleic Acid Atoms Solvent Atoms 994 Heterogen Atoms 150
Software Software Software Name Purpose Blu-Ice data collection REFMAC refinement d*TREK data reduction d*TREK data scaling