☰ Navigation Tabs
horse liver alcohol dehydrogenase complexed with NADH and N-benzyformamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P1R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICRODIALYSIS 7 278 10 mg/ml enzyme dialyzed against 50 mM ammonium N-[tris(hydroxylmethyl)methyl]2-aminoethane sulfonate (pH 6.7 at 25 deg C) with 1 mM NADH and 10 mM N-benzylformamide as the concentration of 2-methyl-2,4-pentanediol was raised to 25 %. Crystas was mounted on a fiber loop and flash vitrified by plunging it into liquid N2.
Crystal Properties Matthews coefficient Solvent content 2.37 48.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.16 α = 90 b = 180.29 β = 106.18 c = 86.92 γ = 90
Symmetry Space Group P 1 21 1
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 210 2006-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.000 APS 17-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 19.95 79.4 0.088 0.094 8.3 6.19 365139
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 59.5 0.513 0.576 1.7 4.34
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 1P1R 1.2 19.95 361271 3775 79.39 0.1586 0.1582 0.1985 0.2306 RANDOM 20.318
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] 1.63 0.19 -1.76 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.882 r_sphericity_free 19.85 r_dihedral_angle_4_deg 14.777 r_dihedral_angle_3_deg 11.714 r_sphericity_bonded 6.595 r_dihedral_angle_1_deg 6.266 r_rigid_bond_restr 3.996 r_angle_refined_deg 2.061 r_angle_other_deg 1.089 r_chiral_restr 0.128
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.882 r_sphericity_free 19.85 r_dihedral_angle_4_deg 14.777 r_dihedral_angle_3_deg 11.714 r_sphericity_bonded 6.595 r_dihedral_angle_1_deg 6.266 r_rigid_bond_restr 3.996 r_angle_refined_deg 2.061 r_angle_other_deg 1.089 r_chiral_restr 0.128 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11140 Nucleic Acid Atoms Solvent Atoms 1357 Heterogen Atoms 240
Software Software Software Name Purpose d*TREK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction O model building d*TREK data reduction