4NG5

V203A 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(hydrozymethyl)methyl]-2-aminoethanesulfonate and 0.5 mM EDTA, pH 6.7 (at 25 deg C), 10 mg/ml protein, 1 mM NAD+, 10 mM 2,3,4,5,6-pentafluorobenzyl alcohol, 13-25 % 2-methyl-2,4-pentanediol, MICRODIALYSIS, temperature 278K
Crystal Properties
Matthews coefficientSolvent content
2.4249.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.52α = 91.8
b = 51.56β = 103.05
c = 92.55γ = 110.3
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDADJUSTABLE FOCUS K-B PAIR SI PLUS PT, RH COATINGS DOUBLE CRYSTAL CRYOCOOLED SI(111)2007-06-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.0332APS23-ID-D

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
11.12086.20.06815.55.2526139910.5
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)
11.11.1454.20.2493.83.4416455

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 4DWV1.117.91261399258723268186.190.119850.119850.119680.13655RANDOM17.529
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]
0.3-0.630.280.420.04-0.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.129
r_sphericity_free36.622
r_dihedral_angle_4_deg11.957
r_dihedral_angle_3_deg11.093
r_sphericity_bonded9.164
r_dihedral_angle_1_deg6.29
r_long_range_B_refined3.713
r_rigid_bond_restr3.337
r_long_range_B_other2.796
r_scangle_other2.343
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.129
r_sphericity_free36.622
r_dihedral_angle_4_deg11.957
r_dihedral_angle_3_deg11.093
r_sphericity_bonded9.164
r_dihedral_angle_1_deg6.29
r_long_range_B_refined3.713
r_rigid_bond_restr3.337
r_long_range_B_other2.796
r_scangle_other2.343
r_scbond_other2.035
r_scbond_it2.033
r_angle_refined_deg1.792
r_mcangle_it1.289
r_mcangle_other1.289
r_mcbond_it1.067
r_mcbond_other1.066
r_angle_other_deg0.885
r_chiral_restr0.105
r_bond_refined_d0.013
r_gen_planes_refined0.008
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 Atoms1052
Heterogen Atoms150

Software

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