5KJE

F322L 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 = 44.37α = 92.02
b = 51.28β = 102.94
c = 92.5γ = 110.01
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDNOIR-12011-04-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 4.2.20.8865ALS4.2.2

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
11.262082.80.0779.43.3416616212.4
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)
11.261.3151.80.3662.43.11

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 REPLACEMENTTHROUGHOUT4DWV1.2620164103158982.720.1240.12380.14416RANDOM18.072
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]
0.28-0.710.60.33-0.41-0.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.592
r_sphericity_free35.998
r_dihedral_angle_4_deg13.665
r_dihedral_angle_3_deg11.548
r_sphericity_bonded10.055
r_dihedral_angle_1_deg6.157
r_long_range_B_refined4.36
r_long_range_B_other3.304
r_scangle_other2.929
r_rigid_bond_restr2.671
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.592
r_sphericity_free35.998
r_dihedral_angle_4_deg13.665
r_dihedral_angle_3_deg11.548
r_sphericity_bonded10.055
r_dihedral_angle_1_deg6.157
r_long_range_B_refined4.36
r_long_range_B_other3.304
r_scangle_other2.929
r_rigid_bond_restr2.671
r_scbond_other2.622
r_scbond_it2.621
r_angle_refined_deg1.872
r_mcangle_it1.662
r_mcangle_other1.662
r_mcbond_it1.389
r_mcbond_other1.389
r_angle_other_deg1.056
r_chiral_restr0.121
r_bond_refined_d0.015
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms5564
Nucleic Acid Atoms
Solvent Atoms972
Heterogen Atoms150

Software

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