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Horse liver alcohol dehydrogenase with NAD and pentafluorobenzyl alcohol at 25 K
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 = 44.42 α = 91.72 b = 51.21 β = 103.12 c = 92.41 γ = 110.22
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 25 CCD ADSC QUANTUM 315r 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) Rrim I (All) Rpim 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 1.2 19.81 93.5 0.046 0.053 0.027 10.7 3.91 216038 10.8
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 1.2 1.24 88.9 0.407 0.469 2.1 3.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4DWV 1.2 19.81 213289 2131 93.17 0.1244 0.1241 0.159 0.1838 RANDOM 16.767
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] 0.35 -0.4 0.31 0.26 0.19 -0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.477 r_dihedral_angle_4_deg 14.213 r_dihedral_angle_3_deg 11.148 r_dihedral_angle_1_deg 6.651 r_rigid_bond_restr 3.626 r_angle_refined_deg 2.077 r_angle_other_deg 1.576 r_chiral_restr 0.12 r_bond_refined_d 0.016 r_gen_planes_refined 0.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.477 r_dihedral_angle_4_deg 14.213 r_dihedral_angle_3_deg 11.148 r_dihedral_angle_1_deg 6.651 r_rigid_bond_restr 3.626 r_angle_refined_deg 2.077 r_angle_other_deg 1.576 r_chiral_restr 0.12 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5570 Nucleic Acid Atoms Solvent Atoms 855 Heterogen Atoms 158
Software Software Software Name Purpose d*TREK data scaling REFMAC refinement PDB_EXTRACT data extraction d*TREK data reduction O model building