5OMO

CRYSTAL STRUCTURE OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE-1 (RPMFE1) COMPLEXED WITH WITH 3S-HYDROXY-DECANOYL-COA AND 3-KETO-DECANOYL-COA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2X58 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6295100MM MES PH 6.0, 150MM AMMONIUM SULPHATE, 15% W/V PEG4000
Crystal Properties
Matthews coefficientSolvent content
2.8156.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.96α = 90
b = 125.08β = 90
c = 223.53γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2010-11-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-40.93928ESRFID14-4

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)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
12.4947.999.20.060.02916.64.464401
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.492.6296.10.280.1584.24

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT2X582.4947.960931320898.730.194460.192710.22831RANDOM53.337
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]
-0.38-2.452.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.622
r_dihedral_angle_4_deg18.859
r_dihedral_angle_3_deg16.153
r_dihedral_angle_1_deg5.924
r_long_range_B_refined4.673
r_long_range_B_other4.673
r_scangle_it2.234
r_scangle_other2.234
r_mcangle_it2.186
r_mcangle_other2.186
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.622
r_dihedral_angle_4_deg18.859
r_dihedral_angle_3_deg16.153
r_dihedral_angle_1_deg5.924
r_long_range_B_refined4.673
r_long_range_B_other4.673
r_scangle_it2.234
r_scangle_other2.234
r_mcangle_it2.186
r_mcangle_other2.186
r_chiral_restr_other1.975
r_angle_refined_deg1.451
r_scbond_it1.298
r_scbond_other1.297
r_mcbond_other1.24
r_mcbond_it1.239
r_angle_other_deg1.039
r_nbd_other0.239
r_symmetry_nbd_refined0.194
r_nbd_refined0.191
r_nbtor_refined0.167
r_symmetry_xyhbond_nbd_refined0.151
r_symmetry_nbd_other0.144
r_xyhbond_nbd_refined0.126
r_ncsr_local_group_10.087
r_chiral_restr0.082
r_symmetry_nbtor_other0.074
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11076
Nucleic Acid Atoms
Solvent Atoms282
Heterogen Atoms228

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
REFMACphasing