4NFH

V207A Horse Liver Alcohol Dehydrogenase E 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 4DWVPDB ENTRY 4DWV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICRODIALYSIS727850 mM ammonium n-[tris(hydroxymethyl) methyl]-2-aminoethane sulfonate, pH 6.7 (at 25 C), 0.25 mM EDTA, 10 mg/ml protein, 1 mM NAD+, 10 mM 2,3,4,5,6-pentafluorobenzyl alcohol, 12 TO 25 % 2-methyl-2,4-pentanediol, MICRODIALYSIS, temperature 278K
Crystal Properties
Matthews coefficientSolvent content
2.448.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.49α = 91.96
b = 51.23β = 103
c = 92.32γ = 110.28
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDNOIR-1Rosenbaum vertical focussing mirrors2008-12-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 4.2.20.827ALS4.2.2

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
11.22094.20.05511.33.7721780711.9
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)
11.21.24740.3632.43.4617131

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 4DWV1.219.84216747106694.140.135470.135470.135320.16569RANDOM16.966
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]
0.24-0.490.240.230.15-0.39
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free41.554
r_dihedral_angle_2_deg38.114
r_dihedral_angle_4_deg14.701
r_dihedral_angle_3_deg11.387
r_sphericity_bonded10.42
r_dihedral_angle_1_deg6.244
r_long_range_B_refined5.096
r_rigid_bond_restr3.921
r_long_range_B_other3.814
r_scangle_other3.088
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free41.554
r_dihedral_angle_2_deg38.114
r_dihedral_angle_4_deg14.701
r_dihedral_angle_3_deg11.387
r_sphericity_bonded10.42
r_dihedral_angle_1_deg6.244
r_long_range_B_refined5.096
r_rigid_bond_restr3.921
r_long_range_B_other3.814
r_scangle_other3.088
r_scbond_it2.764
r_scbond_other2.764
r_angle_refined_deg1.892
r_mcangle_it1.653
r_mcangle_other1.653
r_mcbond_it1.443
r_mcbond_other1.443
r_angle_other_deg0.911
r_chiral_restr0.11
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5566
Nucleic Acid Atoms
Solvent Atoms994
Heterogen Atoms150

Software

Software
Software NamePurpose
Blu-Icedata collection
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling