4DWV

Horse alcohol dehydrogenase complexed with NAD+ and 2,3,4,5,6-pentafluorobenzyl alcohol


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+, 10 mm 2,3,4,5,6-pentafluorobenzyl alcohol, 12 to 25 % 2-methyl-2,4-pentanediol, MICRODIALYSIS, temperature 278k
Crystal Properties
Matthews coefficientSolvent content
2.448.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.29α = 91.72
b = 51.44β = 103.09
c = 92.49γ = 110.11
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDADJUSTABLE FOCUS K-B PAIR SI PLUS PT, RH COATINGS2006-03-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D0.9537APS23-ID-D

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
11.142093.70.06512.94.7527048925339411
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)
11.141.1884.50.2643.23.74

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 1HLD1.1420270489250826257293.650.124060.123870.14373RANDOM14.926
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]
0.11-0.50.210.26-0.06-0.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.256
r_sphericity_free31.716
r_dihedral_angle_4_deg13.883
r_dihedral_angle_3_deg11.32
r_sphericity_bonded9.439
r_dihedral_angle_1_deg6.24
r_scangle_it4.734
r_rigid_bond_restr3.422
r_scbond_it3.168
r_mcangle_it2.191
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.256
r_sphericity_free31.716
r_dihedral_angle_4_deg13.883
r_dihedral_angle_3_deg11.32
r_sphericity_bonded9.439
r_dihedral_angle_1_deg6.24
r_scangle_it4.734
r_rigid_bond_restr3.422
r_scbond_it3.168
r_mcangle_it2.191
r_angle_refined_deg1.673
r_mcbond_it1.479
r_angle_other_deg1.003
r_mcbond_other0.521
r_chiral_restr0.102
r_bond_refined_d0.013
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5570
Nucleic Acid Atoms
Solvent Atoms1040
Heterogen Atoms150

Software

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