4DXH

Horse liver alcohol dehydrogenase complexed with NAD+ and 2,2,2-trifluoroethanol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HLDpdb entry 1HLD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICRODIALYSIS6.727850 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 2,2,2-TRIFLUOROETHANOL, 12 TO 25 % 2-METHYL-2,4-PENTANEDIOL, TEMPERATURE 278K, MICRODIALYSIS
Crystal Properties
Matthews coefficientSolvent content
2.3948.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.25α = 91.91
b = 51.16β = 103.02
c = 92.53γ = 109.9
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rRosenbaum Rock vertical focusing mirror with Pt, glass, Pd lanes2009-06-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9184APS19-ID

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
11.122094.30.0469.74283954267668
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)
11.121.1691.40.3652.14

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1HLD1.1220283954266085135294.140.126630.126530.14672RANDOM13.289
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]
0.16-0.290.190.190.08-0.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.869
r_sphericity_free31.449
r_dihedral_angle_4_deg13.447
r_dihedral_angle_3_deg11.191
r_sphericity_bonded8.924
r_dihedral_angle_1_deg6.142
r_scangle_it4.798
r_scbond_it3.155
r_rigid_bond_restr2.948
r_mcangle_it2.179
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.869
r_sphericity_free31.449
r_dihedral_angle_4_deg13.447
r_dihedral_angle_3_deg11.191
r_sphericity_bonded8.924
r_dihedral_angle_1_deg6.142
r_scangle_it4.798
r_scbond_it3.155
r_rigid_bond_restr2.948
r_mcangle_it2.179
r_angle_refined_deg1.636
r_mcbond_it1.458
r_angle_other_deg0.977
r_mcbond_other0.502
r_chiral_restr0.14
r_bond_refined_d0.011
r_gen_planes_refined0.007
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5570
Nucleic Acid Atoms
Solvent Atoms1025
Heterogen Atoms136

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
d*TREKdata reduction
d*TREKdata scaling
AMoREphasing