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Horse liver alcohol dehydrogenase G173A, complexed with NAD+ and 2,3,4,5,6-pentafluorobenzyl alcohol at 50 K
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5KJ1
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 = 44.3 α = 91.89 b = 51.48 β = 103.04 c = 92.32 γ = 110.16
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 50 CCD ADSC QUANTUM 315r ROSENBAUM ROCK VERTICAL FOCUSINGMIRROR WITH PT, GLASS, PD LANES 2009-06-25 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) 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 1.3 19.98 95.7 0.054 0.062 9.5 3.95 174292
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 1.3 1.35 92.9 0.392 0.453 1.6 3.86
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 5KJ1 1.3 19.98 169833 2564 94.61 0.1301 0.1295 0.1297 0.1669 0.1668 RANDOM 16.301
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] 0.49 -0.35 0.26 0.61 0.03 -1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.211 r_dihedral_angle_4_deg 13.043 r_dihedral_angle_3_deg 11.848 r_dihedral_angle_1_deg 6.802 r_rigid_bond_restr 3.742 r_angle_refined_deg 2.146 r_angle_other_deg 1.58 r_chiral_restr 0.124 r_bond_refined_d 0.017 r_gen_planes_refined 0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.211 r_dihedral_angle_4_deg 13.043 r_dihedral_angle_3_deg 11.848 r_dihedral_angle_1_deg 6.802 r_rigid_bond_restr 3.742 r_angle_refined_deg 2.146 r_angle_other_deg 1.58 r_chiral_restr 0.124 r_bond_refined_d 0.017 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5572 Nucleic Acid Atoms Solvent Atoms 873 Heterogen Atoms 158
Software Software Software Name Purpose REFMAC refinement d*TREK data scaling PDB_EXTRACT data extraction d*TREK data reduction MOLREP phasing