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I220F 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-aminoethanesulfonate, 0.25 mM EDTA, pH 6.7 (at 25 C), 1.0 mM NAD+, 10 mM 2,3,4,5,6-pentafluorbenzyl alcohol, 16 to 25 % 2-methyl-2,4-pentanediol, 10 mg/ml protein in dialysis bag.
Crystal Properties Matthews coefficient Solvent content 2.4 48.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.26 α = 91.75 b = 51.38 β = 103.1 c = 92.39 γ = 109.36
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 2009-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 0.80 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 1.4 20 82.9 0.065 7.9 3.48 119994 18.3
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 1.4 1.43 83.3 0.474 1.8 3.52
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 1.4 20 119994 1803 82.89 0.14237 0.1417 0.1483 0.18709 0.1902 RANDOM 22.459
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] 0.2 0.29 -0.08 0.74 0.18 -1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.483 r_sphericity_free 24.122 r_dihedral_angle_4_deg 15.51 r_dihedral_angle_3_deg 12.321 r_sphericity_bonded 8.341 r_dihedral_angle_1_deg 6.341 r_rigid_bond_restr 6.243 r_long_range_B_refined 3.921 r_long_range_B_other 3.424 r_scangle_other 3.415
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.483 r_sphericity_free 24.122 r_dihedral_angle_4_deg 15.51 r_dihedral_angle_3_deg 12.321 r_sphericity_bonded 8.341 r_dihedral_angle_1_deg 6.341 r_rigid_bond_restr 6.243 r_long_range_B_refined 3.921 r_long_range_B_other 3.424 r_scangle_other 3.415 r_scbond_it 3.241 r_scbond_other 3.241 r_mcangle_it 2.171 r_mcangle_other 2.171 r_mcbond_it 1.966 r_mcbond_other 1.964 r_angle_refined_deg 1.775 r_angle_other_deg 0.88 r_chiral_restr 0.105 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 5576 Nucleic Acid Atoms Solvent Atoms 896 Heterogen Atoms 134
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction d*TREK data scaling O model building REFMAC phasing