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Horse liver alcohol dehydrogense His-51-Gln form complexed with NADH and N-cyclohexylformamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QV6 F51Q/K228R ADH complexed with NAD+ and 2,4-difluorobenzyl alcohol
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICRODIALYSIS 7 278 10 mg/ml protein in 50 mM ammonium N-[tris(hydroxymethyl)methyl]-2-aminoethanesulfate buffer with 0.25 mM EDTA, 1 mM NADH and 15 mM N-cyclohexylformamide, 13 % 2-methyl-2,4-pentanediol,raised to 25% MPD before crystal pliunged into liquid N2.
Crystal Properties Matthews coefficient Solvent content 2.25 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.08 α = 92.1 b = 50.92 β = 102.95 c = 92.74 γ = 109.68
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ confocal 2004-02-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 1.42 19.9 87.9 0.028 0.036 16 2.35 121863
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 1.42 1.47 71.2 0.248 0.324 2.35
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 1qv6 1.42 19.91 119503 2403 87.88 0.14644 0.14554 0.1465 0.19063 0.1594 RANDOM 21.28
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] 0.47 -0.49 0.09 0.26 0.27 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.368 r_dihedral_angle_3_deg 12.526 r_dihedral_angle_4_deg 11.214 r_dihedral_angle_1_deg 6.712 r_rigid_bond_restr 4.258 r_scangle_other 3.849 r_long_range_B_refined 3.802 r_scbond_it 3.769 r_scbond_other 3.769 r_long_range_B_other 3.675
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.368 r_dihedral_angle_3_deg 12.526 r_dihedral_angle_4_deg 11.214 r_dihedral_angle_1_deg 6.712 r_rigid_bond_restr 4.258 r_scangle_other 3.849 r_long_range_B_refined 3.802 r_scbond_it 3.769 r_scbond_other 3.769 r_long_range_B_other 3.675 r_mcangle_it 2.641 r_mcangle_other 2.64 r_mcbond_it 2.386 r_mcbond_other 2.386 r_angle_refined_deg 2.079 r_angle_other_deg 1.555 r_chiral_restr 0.114 r_bond_refined_d 0.017 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5568 Nucleic Acid Atoms Solvent Atoms 640 Heterogen Atoms 118
Software Software Software Name Purpose d*TREK data scaling REFMAC refinement O model building REFMAC phasing d*TREK data processing