5CDU

I220V horse liver alcohol dehydrogenase complexed with NAD and pyrazole


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4DWV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICRODIALYSIS729850 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 PYRAZOLE, 16 TO 25 % 2-METHYL-2,4-PENTANEDIOL
Crystal Properties
Matthews coefficientSolvent content
2.3948.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.23α = 91.88
b = 51.26β = 103.12
c = 92.41γ = 109.95
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
11.62093.40.1230.4146.468978820.1
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)
11.61.6693.70.4142.96.13

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 REPLACEMENTTHROUGHOUT4DWV1.62089788116393.410.161220.160710.20093RANDOM22.272
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]
-0.27-0.130.121.160.31-1.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.724
r_dihedral_angle_4_deg13.432
r_dihedral_angle_3_deg12.934
r_dihedral_angle_1_deg6.427
r_long_range_B_refined6.083
r_long_range_B_other5.732
r_scangle_other4.006
r_scbond_it2.737
r_scbond_other2.736
r_mcangle_it2.186
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.724
r_dihedral_angle_4_deg13.432
r_dihedral_angle_3_deg12.934
r_dihedral_angle_1_deg6.427
r_long_range_B_refined6.083
r_long_range_B_other5.732
r_scangle_other4.006
r_scbond_it2.737
r_scbond_other2.736
r_mcangle_it2.186
r_mcangle_other2.186
r_angle_refined_deg2.012
r_mcbond_it1.674
r_mcbond_other1.673
r_angle_other_deg0.926
r_chiral_restr0.122
r_bond_refined_d0.019
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 Atoms850
Heterogen Atoms118

Software

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