1ZCJ | pdb_00001zcj

Crystal structure of 3-hydroxyacyl-CoA dehydrogenase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1WDK1wdk alpha subunit

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5295PEG 4000, tri-Na citrate, ammonium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.1643

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.91α = 90
b = 122.91β = 90
c = 58.25γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2002-09-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I7111.134MAX III711

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.93037374

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 REPLACEMENTTHROUGHOUT1wdk alpha subunit1.93034648111599.980.171410.169780.170.220690.21RANDOM19.595
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]
-0.36-0.360.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.181
r_scangle_it3.57
r_scbond_it2.325
r_angle_refined_deg1.68
r_mcangle_it1.439
r_mcbond_it0.814
r_nbd_refined0.235
r_symmetry_vdw_refined0.19
r_xyhbond_nbd_refined0.185
r_symmetry_hbond_refined0.155
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.181
r_scangle_it3.57
r_scbond_it2.325
r_angle_refined_deg1.68
r_mcangle_it1.439
r_mcbond_it0.814
r_nbd_refined0.235
r_symmetry_vdw_refined0.19
r_xyhbond_nbd_refined0.185
r_symmetry_hbond_refined0.155
r_chiral_restr0.098
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3559
Nucleic Acid Atoms
Solvent Atoms582
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
XDSdata scaling
PHASERphasing