8G2X

Horse liver alcohol dehydrogense His-51-Gln form complexed with NAD+ and pyrazole


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1N92 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE727810 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 pyrazole, 13 % 2-methyl-2,4-pentanediol, raised to 25% MPD before pliunging into liquid N2.
Crystal Properties
Matthews coefficientSolvent content
2.2445

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.13α = 92.09
b = 50.8β = 102.96
c = 92.41γ = 109.68
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++confocal2003-04-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
11.4719.9890.10.0290.04114.31.95112102
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)
11.471.5283.10.2480.3511.92

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 REPLACEMENTTHROUGHOUT1N921.4719.99110430165990.080.173430.173170.19092RANDOM18.302
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]
0.07-0.850.211.050.26-0.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.495
r_dihedral_angle_3_deg12.017
r_dihedral_angle_4_deg11.333
r_dihedral_angle_1_deg6.818
r_long_range_B_refined4.677
r_long_range_B_other4.457
r_scangle_other3.549
r_scbond_it2.395
r_scbond_other2.395
r_mcangle_it1.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.495
r_dihedral_angle_3_deg12.017
r_dihedral_angle_4_deg11.333
r_dihedral_angle_1_deg6.818
r_long_range_B_refined4.677
r_long_range_B_other4.457
r_scangle_other3.549
r_scbond_it2.395
r_scbond_other2.395
r_mcangle_it1.93
r_mcangle_other1.93
r_angle_refined_deg1.878
r_angle_other_deg1.493
r_mcbond_it1.41
r_mcbond_other1.409
r_chiral_restr0.096
r_bond_refined_d0.013
r_gen_planes_refined0.01
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5568
Nucleic Acid Atoms
Solvent Atoms696
Heterogen Atoms118

Software

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