8G2S

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1N8K 

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 1 mM sodium caprate, 13 % 2-methyl-2,4-pentanediol, raised to 25% MPD, then crystals soaked with 1 mM acetaldehyde at 278 K for 70 min and then with 100 mM sodium caprate for 2 h before pliunging into liquid N2.
Crystal Properties
Matthews coefficientSolvent content
2.2646

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.24α = 92.01
b = 51.25β = 102.87
c = 92.46γ = 109.91
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVconfocal2004-05-18MSINGLE 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
11.4519.9887.40.0330.03923.83.79114498
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)
11.451.552.10.210.2483.55

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 REPLACEMENTTHROUGHOUT1n8k1.4519.98112223227287.380.156890.156240.18912RANDOM14.575
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]
0.51-0.520.180.46-0.02-0.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.896
r_dihedral_angle_3_deg12.332
r_dihedral_angle_4_deg11.235
r_dihedral_angle_1_deg6.743
r_long_range_B_refined4.208
r_long_range_B_other3.964
r_scangle_other3.018
r_scbond_it2.04
r_scbond_other2.039
r_angle_refined_deg1.989
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.896
r_dihedral_angle_3_deg12.332
r_dihedral_angle_4_deg11.235
r_dihedral_angle_1_deg6.743
r_long_range_B_refined4.208
r_long_range_B_other3.964
r_scangle_other3.018
r_scbond_it2.04
r_scbond_other2.039
r_angle_refined_deg1.989
r_mcangle_it1.686
r_mcangle_other1.686
r_angle_other_deg1.499
r_mcbond_it1.19
r_mcbond_other1.189
r_chiral_restr0.101
r_bond_refined_d0.013
r_gen_planes_refined0.01
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms751
Heterogen Atoms140

Software

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