5CDS

I220L 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-,4-PENTANEDIOL
Crystal Properties
Matthews coefficientSolvent content
2.2846

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.27α = 91.75
b = 51.53β = 103.12
c = 92.44γ = 109.34
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
11.420910.05111.33.64132451
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)
11.41.43686.770.3732.33.61

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 REPLACEMENTTHROUGHOUT4DWV1.420132451134091.040.132460.131940.18411RANDOM23.44
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]
0.140.63-0.141.57-0.08-2.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.867
r_sphericity_free30.412
r_dihedral_angle_4_deg15.474
r_dihedral_angle_3_deg12.072
r_sphericity_bonded10.302
r_dihedral_angle_1_deg6.317
r_long_range_B_refined4.378
r_scangle_other3.899
r_long_range_B_other3.789
r_rigid_bond_restr3.726
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.867
r_sphericity_free30.412
r_dihedral_angle_4_deg15.474
r_dihedral_angle_3_deg12.072
r_sphericity_bonded10.302
r_dihedral_angle_1_deg6.317
r_long_range_B_refined4.378
r_scangle_other3.899
r_long_range_B_other3.789
r_rigid_bond_restr3.726
r_scbond_other3.581
r_scbond_it3.575
r_mcangle_it2.356
r_mcangle_other2.356
r_mcbond_it2.127
r_mcbond_other2.127
r_angle_refined_deg1.702
r_angle_other_deg0.877
r_chiral_restr0.101
r_bond_refined_d0.014
r_gen_planes_refined0.008
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5570
Nucleic Acid Atoms
Solvent Atoms864
Heterogen Atoms134

Software

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