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G173A 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+, 10 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 = 44.31 α = 91.82 b = 51.5 β = 103.05 c = 92.42 γ = 110.12
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 85 CCD ADSC QUANTUM 315r ROSENBAUM ROCK VERTICAL FOCUSING MIRROR WITH PT, GLASS, PD LANES 2009-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9184 APS 19-ID
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 94.6 0.066 9.2 3.95 220050 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 1.2 1.24 91.9 0.486 2.1 3.87
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 1.2 20 218364 1099 94.56 0.12402 0.1238 0.1237 0.16995 0.1692 RANDOM 16.997
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] 0.31 -0.35 0.33 0.57 0.11 -0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.925 r_sphericity_free 30.732 r_dihedral_angle_4_deg 13.674 r_dihedral_angle_3_deg 11.659 r_sphericity_bonded 8.439 r_dihedral_angle_1_deg 6.424 r_long_range_B_refined 3.674 r_rigid_bond_restr 3.327 r_long_range_B_other 2.815 r_scangle_other 2.326
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.925 r_sphericity_free 30.732 r_dihedral_angle_4_deg 13.674 r_dihedral_angle_3_deg 11.659 r_sphericity_bonded 8.439 r_dihedral_angle_1_deg 6.424 r_long_range_B_refined 3.674 r_rigid_bond_restr 3.327 r_long_range_B_other 2.815 r_scangle_other 2.326 r_scbond_other 2.073 r_scbond_it 2.071 r_angle_refined_deg 1.966 r_mcangle_other 1.51 r_mcangle_it 1.509 r_mcbond_it 1.284 r_mcbond_other 1.283 r_angle_other_deg 1.078 r_chiral_restr 0.116 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 r_gen_planes_other 0.003 r_bond_other_d 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 1016 Heterogen Atoms 150
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction d*TREK data scaling REFMAC phasing