1YXM

Crystal structure of peroxisomal trans 2-enoyl CoA reductase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1VL8PDB entry 1VL8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5294Ammonium sulphate, Sodium chloride, Sodium cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.243.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.152α = 90
b = 119.014β = 90
c = 119.909γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42005-01-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.11ALS8.3.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.947.3598.30.0464210885118851133
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.92.0696.90.4453

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1VL81.9478198581985430297.490.206210.206210.204170.24459RANDOM33.504
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]
-0.020.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.773
r_dihedral_angle_3_deg13.487
r_dihedral_angle_1_deg12.739
r_dihedral_angle_4_deg11.128
r_scangle_it3.659
r_scbond_it2.531
r_angle_refined_deg1.676
r_mcangle_it1.648
r_mcbond_it1.006
r_angle_other_deg0.879
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.773
r_dihedral_angle_3_deg13.487
r_dihedral_angle_1_deg12.739
r_dihedral_angle_4_deg11.128
r_scangle_it3.659
r_scbond_it2.531
r_angle_refined_deg1.676
r_mcangle_it1.648
r_mcbond_it1.006
r_angle_other_deg0.879
r_mcbond_other0.422
r_symmetry_hbond_refined0.349
r_nbd_refined0.217
r_nbtor_refined0.183
r_nbd_other0.18
r_xyhbond_nbd_refined0.173
r_symmetry_vdw_other0.172
r_symmetry_vdw_refined0.169
r_chiral_restr0.106
r_nbtor_other0.089
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8288
Nucleic Acid Atoms
Solvent Atoms374
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing