2VRE

crystal structure of human peroxisomal delta3,5,delta2,4-dienoyl coa isomerase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.2M CA(AC)2, 0.1M CACODYLATE PH 6.5, 18% PEG 8K
Crystal Properties
Matthews coefficientSolvent content
2.3146.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 127.58α = 90
b = 137.253β = 90
c = 96.137γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2008-03-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SASLSX10SA

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
11.9593.2599.80.0810.33.758508
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)
11.9521000.6323.7

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1DCI1.9593.255850831321000.1690.1670.202RANDOM37.71
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]
-0.96-0.291.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.188
r_dihedral_angle_4_deg15.276
r_dihedral_angle_3_deg14.115
r_scangle_it6.799
r_dihedral_angle_1_deg6.104
r_scbond_it4.711
r_mcangle_it2.641
r_mcbond_it1.706
r_angle_refined_deg1.348
r_chiral_restr0.101
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.188
r_dihedral_angle_4_deg15.276
r_dihedral_angle_3_deg14.115
r_scangle_it6.799
r_dihedral_angle_1_deg6.104
r_scbond_it4.711
r_mcangle_it2.641
r_mcbond_it1.706
r_angle_refined_deg1.348
r_chiral_restr0.101
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6005
Nucleic Acid Atoms
Solvent Atoms393
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing