5KJ1 | pdb_00005kj1

G173A horse liver 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
2.2646

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.31α = 91.82
b = 51.5β = 103.05
c = 92.42γ = 110.12
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray85CCDADSC QUANTUM 315rROSENBAUM ROCK VERTICAL FOCUSING MIRROR WITH PT, GLASS, PD LANES2009-06-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9184APS19-ID

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
11.22094.60.0669.23.9522005010.2
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)
11.21.2491.90.4862.13.87

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4DWV1.220218364109994.560.124020.12380.120.169950.17RANDOM16.997
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]
0.31-0.350.330.570.11-0.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.925
r_sphericity_free30.732
r_dihedral_angle_4_deg13.674
r_dihedral_angle_3_deg11.659
r_sphericity_bonded8.439
r_dihedral_angle_1_deg6.424
r_long_range_B_refined3.674
r_rigid_bond_restr3.327
r_long_range_B_other2.815
r_scangle_other2.326
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.925
r_sphericity_free30.732
r_dihedral_angle_4_deg13.674
r_dihedral_angle_3_deg11.659
r_sphericity_bonded8.439
r_dihedral_angle_1_deg6.424
r_long_range_B_refined3.674
r_rigid_bond_restr3.327
r_long_range_B_other2.815
r_scangle_other2.326
r_scbond_other2.073
r_scbond_it2.071
r_angle_refined_deg1.966
r_mcangle_other1.51
r_mcangle_it1.509
r_mcbond_it1.284
r_mcbond_other1.283
r_angle_other_deg1.078
r_chiral_restr0.116
r_bond_refined_d0.017
r_gen_planes_refined0.01
r_gen_planes_other0.003
r_bond_other_d0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5572
Nucleic Acid Atoms
Solvent Atoms1016
Heterogen Atoms150

Software

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