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Horse liver alcohol dehydrogense His-51-Gln form complexed with NADH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8G2L H51Q ADH with NAD+ and trifluoroethanol
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, 2 mM NAD+ and 0.1 mM 2,2,2-trifluoroetanol, crystals formed at 13 % 2-methyl-2,4-pentanediol, raised to 25% MPD before crystal pliunged into liquid N2.
Crystal Properties Matthews coefficient Solvent content 2.26 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.06 α = 91.9 b = 51.32 β = 103.08 c = 92.75 γ = 109.89
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 2004-05-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU R-AXIS IV 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 1.5 19.91 91.2 0.031 0.036 25 3.84 107864
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 1.5 1.55 84.9 0.17 0.199 3.75
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 8g2l 1.5 19.91 105749 2114 91.13 0.15551 0.15508 0.17722 0.1965 RANDOM 14.969
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] 0.43 -0.42 0.23 0.5 0.1 -0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.711 r_dihedral_angle_3_deg 12.511 r_dihedral_angle_4_deg 11.575 r_dihedral_angle_1_deg 6.914 r_long_range_B_refined 4.113 r_long_range_B_other 3.96 r_scangle_other 3.184 r_scbond_it 2.154 r_scbond_other 2.153 r_angle_refined_deg 1.939
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.711 r_dihedral_angle_3_deg 12.511 r_dihedral_angle_4_deg 11.575 r_dihedral_angle_1_deg 6.914 r_long_range_B_refined 4.113 r_long_range_B_other 3.96 r_scangle_other 3.184 r_scbond_it 2.154 r_scbond_other 2.153 r_angle_refined_deg 1.939 r_mcangle_it 1.77 r_mcangle_other 1.77 r_angle_other_deg 1.51 r_mcbond_it 1.29 r_mcbond_other 1.29 r_chiral_restr 0.099 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5568 Nucleic Acid Atoms Solvent Atoms 663 Heterogen Atoms 124
Software Software Software Name Purpose d*TREK data scaling REFMAC refinement O model building REFMAC phasing d*TREK data processing