5CDG

I220F 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-aminoethanesulfonate, 0.25 mM EDTA, pH 6.7 (at 25 C), 1.0 mM NAD+, 10 mM 2,3,4,5,6-pentafluorbenzyl alcohol, 16 to 25 % 2-methyl-2,4-pentanediol, 10 mg/ml protein in dialysis bag.
Crystal Properties
Matthews coefficientSolvent content
2.448.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.26α = 91.75
b = 51.38β = 103.1
c = 92.39γ = 109.36
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDNOIR-12009-01-28MSINGLE 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
11.42082.90.0657.93.4811999418.3
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)
11.41.4383.30.4741.83.52

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 REPLACEMENTTHROUGHOUT4DWV1.420119994180382.890.142370.14170.18709RANDOM22.459
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]
0.20.29-0.080.740.18-1.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.483
r_sphericity_free24.122
r_dihedral_angle_4_deg15.51
r_dihedral_angle_3_deg12.321
r_sphericity_bonded8.341
r_dihedral_angle_1_deg6.341
r_rigid_bond_restr6.243
r_long_range_B_refined3.921
r_long_range_B_other3.424
r_scangle_other3.415
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.483
r_sphericity_free24.122
r_dihedral_angle_4_deg15.51
r_dihedral_angle_3_deg12.321
r_sphericity_bonded8.341
r_dihedral_angle_1_deg6.341
r_rigid_bond_restr6.243
r_long_range_B_refined3.921
r_long_range_B_other3.424
r_scangle_other3.415
r_scbond_it3.241
r_scbond_other3.241
r_mcangle_it2.171
r_mcangle_other2.171
r_mcbond_it1.966
r_mcbond_other1.964
r_angle_refined_deg1.775
r_angle_other_deg0.88
r_chiral_restr0.105
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5576
Nucleic Acid Atoms
Solvent Atoms896
Heterogen Atoms134

Software

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