5CDT

I220V 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
2.448.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.3α = 91.92
b = 51.5β = 103.09
c = 92.35γ = 110.17
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDNOIR-12009-03-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 4.2.20.80ALS4.2.2

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
11.72096.40.08573.237745921.2
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)
11.71.74494.40.3442.33.15

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 REPLACEMENTTHROUGHOUT4DWV1.72077459113496.390.162730.162110.20569RANDOM23.112
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]
-0.2-0.270.311.36-0.18-1.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.453
r_dihedral_angle_4_deg15.342
r_dihedral_angle_3_deg13.316
r_dihedral_angle_1_deg6.568
r_long_range_B_refined5.982
r_long_range_B_other5.553
r_scangle_other4.103
r_scbond_it2.774
r_scbond_other2.774
r_mcangle_other2.328
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.453
r_dihedral_angle_4_deg15.342
r_dihedral_angle_3_deg13.316
r_dihedral_angle_1_deg6.568
r_long_range_B_refined5.982
r_long_range_B_other5.553
r_scangle_other4.103
r_scbond_it2.774
r_scbond_other2.774
r_mcangle_other2.328
r_mcangle_it2.327
r_angle_refined_deg2.039
r_mcbond_it1.791
r_mcbond_other1.79
r_angle_other_deg0.955
r_chiral_restr0.122
r_bond_refined_d0.02
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 Atoms838
Heterogen Atoms134

Software

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