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Horse liver alcohol dehydrogenase with NAD and pentafluorobenzyl alcohol at 100 K, 1.2 A, crystal 16
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7UDR
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 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.31 α = 91.9 b = 51.27 β = 103.01 c = 92.52 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 100 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) 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 20 95.1 0.052 0.06 0.03 8.8 4.05 219960 10.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.24 92.5 0.522 0.601 0.298 1 4.07
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 7udr 1.2 20 215093 2141 93.89 0.127 0.1268 0.1269 0.1504 0.1502 RANDOM 15.709
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] 0.32 -0.42 0.33 0.31 0.1 -0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.388 r_dihedral_angle_4_deg 14.304 r_dihedral_angle_3_deg 11.215 r_dihedral_angle_1_deg 6.642 r_rigid_bond_restr 3.438 r_angle_refined_deg 2.041 r_angle_other_deg 1.554 r_chiral_restr 0.123 r_bond_refined_d 0.016 r_gen_planes_refined 0.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.388 r_dihedral_angle_4_deg 14.304 r_dihedral_angle_3_deg 11.215 r_dihedral_angle_1_deg 6.642 r_rigid_bond_restr 3.438 r_angle_refined_deg 2.041 r_angle_other_deg 1.554 r_chiral_restr 0.123 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 REFMAC phasing