6O91

Horse liver L57F alcohol dehydrogenase complexed with NAD and pentafluorobenzyl alcohol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 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
Crystal Properties
Matthews coefficientSolvent content
2.4148.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.5α = 91.8
b = 51.52β = 103.07
c = 92.54γ = 110.42
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDADJUSTABLE FOCUS K-B PAIR 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
11.0919.89880.1030.113105.52273671
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)
11.091.1350.20.2420.2853.43.51

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 REPLACEMENTTHROUGHOUT4DWV1.119.9267504263989.280.11840.11830.1324RANDOM15.169
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]
0.27-0.770.190.63-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.788
r_dihedral_angle_1_deg17.649
r_dihedral_angle_4_deg16.422
r_dihedral_angle_3_deg11.187
r_rigid_bond_restr2.327
r_angle_refined_deg1.836
r_angle_other_deg1.541
r_chiral_restr0.106
r_bond_refined_d0.012
r_gen_planes_refined0.009
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.788
r_dihedral_angle_1_deg17.649
r_dihedral_angle_4_deg16.422
r_dihedral_angle_3_deg11.187
r_rigid_bond_restr2.327
r_angle_refined_deg1.836
r_angle_other_deg1.541
r_chiral_restr0.106
r_bond_refined_d0.012
r_gen_planes_refined0.009
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5576
Nucleic Acid Atoms
Solvent Atoms1138
Heterogen Atoms174

Software

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