3OQ6

Horse liver alcohol dehydrogenase A317C mutant complexed with NAD+ and 2,3,4,5,6-pentafluorobenzyl alcohol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HLDPDB entry 1hld

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICRODIALYSIS729850 mM ammonium TES [N-tris(hydroxymethyl)-2-aminoethane sulfonate], 25% MRD, 11 mg/ml protein, 11 mM NAD+, 5 mM 2,3,4,5,6-pentafluorobenzyl alcohol, pH 7.0, MICRODIALYSIS, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3948.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.34α = 91.98
b = 51.31β = 102.95
c = 92.21γ = 110.11
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDNOIR-1SAGGITALLY FOCUSED MIRRORS2009-03-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 4.2.20.80ALS4.2.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.29092.20.0619.43.5721421311.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.21.2483.60.28133.4319347

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 REPLACEMENTTHROUGHOUTPDB entry 1hld1.219.85214172106192.290.13510.1350.1621RANDOM17.5778
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]
-0.19-0.310.41-0.320.120.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.981
r_dihedral_angle_4_deg12.894
r_dihedral_angle_3_deg11.074
r_dihedral_angle_1_deg6.182
r_scangle_it4.959
r_scbond_it3.343
r_mcangle_it2.344
r_angle_refined_deg1.616
r_mcbond_it1.581
r_rigid_bond_restr1.331
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.981
r_dihedral_angle_4_deg12.894
r_dihedral_angle_3_deg11.074
r_dihedral_angle_1_deg6.182
r_scangle_it4.959
r_scbond_it3.343
r_mcangle_it2.344
r_angle_refined_deg1.616
r_mcbond_it1.581
r_rigid_bond_restr1.331
r_angle_other_deg0.989
r_mcbond_other0.84
r_chiral_restr0.096
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5572
Nucleic Acid Atoms
Solvent Atoms1098
Heterogen Atoms142

Software

Software
Software NamePurpose
d*TREKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
d*TREKdata reduction