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Horse liver F93W alcohol dehydrogenase complexed with NAD and pentafluorobenzyl alcohol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6O91
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICRODIALYSIS 7 298 10 mg/ml protein, 50 mM ammonium N-[tris(hydroxymethyl)methyl]-2-aminoethane sulfonate, 0.25 mM EDTA, pH 6.7 at 25 deg C, 1 mM NAD+, 10 mM 2,3,4,5,6-pentafluorobenzyl alcohol, 14 to 25 % 2-methyl-2,4-pentanediol
Crystal Properties Matthews coefficient Solvent content 2.41 48.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.47 α = 92.09 b = 51.44 β = 102.95 c = 92.56 γ = 110.25
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 300 mm CCD adjustable foculs K-B pari SiPlus PT, RH coatings 2007-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.0332 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.1 19.62 88.6 0.075 0.082 11.4 5.15 267734
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.1 1.14 56.8 0.28 0.329 3.1 3.44
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 6o91 1.1 19.62 265082 2622 88.55 0.12402 0.12386 0.1238 0.14059 0.1408 RANDOM 15.811
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] 0.14 -0.54 0.31 0.46 0.12 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.794 r_dihedral_angle_1_deg 17.844 r_dihedral_angle_4_deg 13.531 r_dihedral_angle_3_deg 10.888 r_long_range_B_refined 2.589 r_rigid_bond_restr 2.481 r_long_range_B_other 2.165 r_scangle_other 1.945 r_angle_refined_deg 1.843 r_scbond_it 1.676
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.794 r_dihedral_angle_1_deg 17.844 r_dihedral_angle_4_deg 13.531 r_dihedral_angle_3_deg 10.888 r_long_range_B_refined 2.589 r_rigid_bond_restr 2.481 r_long_range_B_other 2.165 r_scangle_other 1.945 r_angle_refined_deg 1.843 r_scbond_it 1.676 r_scbond_other 1.675 r_angle_other_deg 1.541 r_mcangle_it 1.204 r_mcangle_other 1.204 r_mcbond_it 0.987 r_mcbond_other 0.985 r_chiral_restr 0.107 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 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 r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5576 Nucleic Acid Atoms Solvent Atoms 1024 Heterogen Atoms 142
Software Software Software Name Purpose REFMAC refinement d*TREK data scaling PDB_EXTRACT data extraction REFMAC phasing O model building d*TREK data reduction