8G4V

Horse liver alcohol dehydrogense His-51-Gln form 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 4DWV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICRODIALYSIS727810 mg/ml protein in 50 mM ammonium N-[tris(hydroxymethyl)methyl]-2-aminoethanesulfate buffer with 0.25 mM EDTA, 2 mM NAD+ and 15 mM 2,3,4,5,6-pentafluorobenzyl alcohol, crystals formed at ~13 % 2-methyl-2,4-pentanediol, raised to 25% MPD before crystal pliunged into liquid N2.
Crystal Properties
Matthews coefficientSolvent content
2.2846

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.17α = 92.02
b = 51.59β = 102.89
c = 92.77γ = 110.04
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102004-07-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.000APS17-ID

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
11.219.9691.10.060.06513.36.13211946
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)
11.21.2474.40.1810.2123.5

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 REPLACEMENTTHROUGHOUT4dwv1.219.96207414209189.980.135180.134930.1607RANDOM17.445
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]
0.19-0.330.060.530.11-0.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.392
r_dihedral_angle_4_deg13.729
r_dihedral_angle_3_deg12.183
r_dihedral_angle_1_deg6.595
r_rigid_bond_restr4.988
r_scangle_other3.215
r_scbond_it3.139
r_scbond_other3.139
r_long_range_B_refined2.968
r_long_range_B_other2.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.392
r_dihedral_angle_4_deg13.729
r_dihedral_angle_3_deg12.183
r_dihedral_angle_1_deg6.595
r_rigid_bond_restr4.988
r_scangle_other3.215
r_scbond_it3.139
r_scbond_other3.139
r_long_range_B_refined2.968
r_long_range_B_other2.85
r_angle_refined_deg2.256
r_mcangle_it1.719
r_mcangle_other1.719
r_angle_other_deg1.582
r_mcbond_it1.551
r_mcbond_other1.549
r_chiral_restr0.139
r_bond_refined_d0.02
r_gen_planes_refined0.013
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms5568
Nucleic Acid Atoms
Solvent Atoms673
Heterogen Atoms126

Software

Software
Software NamePurpose
d*TREKdata scaling
REFMACrefinement
d*TREKdata reduction
Omodel building