5KCP | pdb_00005kcp

horse liver S48T 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+, 100 mM 2,3,4,5,6-PENTAFLUOROBENZYL ALCOHOL, 12 TO 25 % 2-METHYL-2,4-PENTANEDIOL
Crystal Properties
Matthews coefficientSolvent content
2.2846

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.44α = 91.87
b = 51.59β = 103.06
c = 92.56γ = 110.33
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDADJUSTABLE FOCUS K-B PAIR SIPLUS PT, RH COATINGS2007-06-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1.0332APS23-ID-B

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
11.119.489.30.06115.55.5227042010.2
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)
11.11.1456.70.1855.13.5

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4DWV1.119.4269109130589.310.117840.117750.120.138050.14RANDOM16.86
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]
0.4-0.520.330.41-0.02-0.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.89
r_sphericity_free26.985
r_dihedral_angle_4_deg13.496
r_dihedral_angle_3_deg10.582
r_sphericity_bonded8.098
r_dihedral_angle_1_deg6.244
r_long_range_B_refined3.394
r_long_range_B_other2.566
r_rigid_bond_restr2.053
r_scangle_other1.884
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.89
r_sphericity_free26.985
r_dihedral_angle_4_deg13.496
r_dihedral_angle_3_deg10.582
r_sphericity_bonded8.098
r_dihedral_angle_1_deg6.244
r_long_range_B_refined3.394
r_long_range_B_other2.566
r_rigid_bond_restr2.053
r_scangle_other1.884
r_angle_refined_deg1.726
r_scbond_it1.608
r_scbond_other1.608
r_mcangle_it1.191
r_mcangle_other1.191
r_angle_other_deg0.987
r_mcbond_it0.95
r_mcbond_other0.949
r_chiral_restr0.099
r_bond_refined_d0.012
r_gen_planes_refined0.008
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 Atoms5572
Nucleic Acid Atoms
Solvent Atoms1043
Heterogen Atoms176

Software

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