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Horse liver alcohol dehydrogenase with NAD and pentafluorobenzyl alcohol at 85 K
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 = 44.28 α = 91.81 b = 51.27 β = 103.05 c = 92.5 γ = 110.05
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 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 1.2 19.98 94.6 0.04 0.055 8.9 2.04 218760
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 92.4 0.301 0.417 2 2.05
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 7udr 1.2 19.98 215003 3198 94.36 0.1236 0.1233 0.1475 0.1611 RANDOM 14.815
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] 0.27 -0.51 0.27 0.33 0.05 -0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.634 r_dihedral_angle_4_deg 14.505 r_dihedral_angle_3_deg 11.136 r_dihedral_angle_1_deg 6.735 r_rigid_bond_restr 3.227 r_angle_refined_deg 2.01 r_angle_other_deg 1.551 r_chiral_restr 0.117 r_bond_refined_d 0.015 r_gen_planes_refined 0.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.634 r_dihedral_angle_4_deg 14.505 r_dihedral_angle_3_deg 11.136 r_dihedral_angle_1_deg 6.735 r_rigid_bond_restr 3.227 r_angle_refined_deg 2.01 r_angle_other_deg 1.551 r_chiral_restr 0.117 r_bond_refined_d 0.015 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