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V197I Horse liver alcohol dehydrogenase complexed with NAD+ and pentafluorobenzyl alcohol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 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+, 19 MM 2,3,4,5,6-PENTAFLUOROBENZYL ALCOHOL, 12 TO 25 % 2-METHYL-2,4-PENTANEDIOL
Crystal Properties Matthews coefficient Solvent content 2.26 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.47 α = 91.92 b = 51.65 β = 103.01 c = 92.68 γ = 110.17
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 2008-01-01 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 1.14 20 86 0.047 14.8 3.43 234800 9.9
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 1.14 1.18 51.1 0.384 2.3 3.2
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 4DWV 1.14 20 233565 1172 85.92 0.13654 0.1364 0.145 0.16415 0.1701 RANDOM 17.159
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] 0.3 -0.27 0.34 0.27 0.24 -0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.197 r_sphericity_free 29.932 r_dihedral_angle_4_deg 14.03 r_dihedral_angle_3_deg 11.66 r_sphericity_bonded 8.54 r_dihedral_angle_1_deg 6.331 r_rigid_bond_restr 4.87 r_long_range_B_refined 3.593 r_long_range_B_other 2.901 r_scangle_other 2.701
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.197 r_sphericity_free 29.932 r_dihedral_angle_4_deg 14.03 r_dihedral_angle_3_deg 11.66 r_sphericity_bonded 8.54 r_dihedral_angle_1_deg 6.331 r_rigid_bond_restr 4.87 r_long_range_B_refined 3.593 r_long_range_B_other 2.901 r_scangle_other 2.701 r_scbond_other 2.457 r_scbond_it 2.453 r_angle_refined_deg 2.194 r_mcangle_it 1.638 r_mcangle_other 1.637 r_angle_other_deg 1.517 r_mcbond_it 1.433 r_mcbond_other 1.433 r_chiral_restr 0.131 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5572 Nucleic Acid Atoms Solvent Atoms 973 Heterogen Atoms 150
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction d*TREK data scaling REFMAC phasing