6OWM

Horse liver F93W alcohol dehydrogenase complexed with NAD and pentafluorobenzyl alcohol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6O91 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICRODIALYSIS729810 mg/ml protein, 50 mM ammonium N-[tris(hydroxymethyl)methyl]-2-aminoethane sulfonate, 0.25 mM EDTA, pH 6.7 at 25 deg C, 1 mM NAD+, 10 mM 2,3,4,5,6-pentafluorobenzyl alcohol, 14 to 25 % 2-methyl-2,4-pentanediol
Crystal Properties
Matthews coefficientSolvent content
2.4148.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.47α = 92.09
b = 51.44β = 102.95
c = 92.56γ = 110.25
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDadjustable foculs K-B pari SiPlus PT, RH coatings2007-06-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1.0332APS23-ID-B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.119.6288.60.0750.08211.45.15267734
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)RedundancyNumber Unique Reflections (All)
11.11.1456.80.280.3293.13.44

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6o911.119.62265082262288.550.124020.123860.14059RANDOM15.811
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]
0.14-0.540.310.460.12-0.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.794
r_dihedral_angle_1_deg17.844
r_dihedral_angle_4_deg13.531
r_dihedral_angle_3_deg10.888
r_long_range_B_refined2.589
r_rigid_bond_restr2.481
r_long_range_B_other2.165
r_scangle_other1.945
r_angle_refined_deg1.843
r_scbond_it1.676
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.794
r_dihedral_angle_1_deg17.844
r_dihedral_angle_4_deg13.531
r_dihedral_angle_3_deg10.888
r_long_range_B_refined2.589
r_rigid_bond_restr2.481
r_long_range_B_other2.165
r_scangle_other1.945
r_angle_refined_deg1.843
r_scbond_it1.676
r_scbond_other1.675
r_angle_other_deg1.541
r_mcangle_it1.204
r_mcangle_other1.204
r_mcbond_it0.987
r_mcbond_other0.985
r_chiral_restr0.107
r_bond_refined_d0.013
r_gen_planes_refined0.009
r_gen_planes_other0.002
r_bond_other_d0.001
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 AtomsNumber
Protein Atoms5576
Nucleic Acid Atoms
Solvent Atoms1024
Heterogen Atoms142

Software

Software
Software NamePurpose
REFMACrefinement
d*TREKdata scaling
PDB_EXTRACTdata extraction
REFMACphasing
Omodel building
d*TREKdata reduction