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horse liver S48T 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+, 100 mM 2,3,4,5,6-PENTAFLUOROBENZYL ALCOHOL, 12 TO 25 % 2-METHYL-2,4-PENTANEDIOL
Crystal Properties Matthews coefficient Solvent content 2.28 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.44 α = 91.87 b = 51.59 β = 103.06 c = 92.56 γ = 110.33
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 FOCUS K-B PAIR 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) 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 19.4 89.3 0.061 15.5 5.52 270420 10.2
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 1.1 1.14 56.7 0.185 5.1 3.5
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 1.1 19.4 269109 1305 89.31 0.11784 0.11775 0.1174 0.13805 0.1371 RANDOM 16.86
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] 0.4 -0.52 0.33 0.41 -0.02 -0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.89 r_sphericity_free 26.985 r_dihedral_angle_4_deg 13.496 r_dihedral_angle_3_deg 10.582 r_sphericity_bonded 8.098 r_dihedral_angle_1_deg 6.244 r_long_range_B_refined 3.394 r_long_range_B_other 2.566 r_rigid_bond_restr 2.053 r_scangle_other 1.884
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.89 r_sphericity_free 26.985 r_dihedral_angle_4_deg 13.496 r_dihedral_angle_3_deg 10.582 r_sphericity_bonded 8.098 r_dihedral_angle_1_deg 6.244 r_long_range_B_refined 3.394 r_long_range_B_other 2.566 r_rigid_bond_restr 2.053 r_scangle_other 1.884 r_angle_refined_deg 1.726 r_scbond_it 1.608 r_scbond_other 1.608 r_mcangle_it 1.191 r_mcangle_other 1.191 r_angle_other_deg 0.987 r_mcbond_it 0.95 r_mcbond_other 0.949 r_chiral_restr 0.099 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 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 1043 Heterogen Atoms 176
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction d*TREK data scaling REFMAC phasing