5MGB

Crystal Structure of Rat Peroxisomal Multifunctional enzyme Type-1 (RPMFE1) Complexed with Acetoacetyl-CoA and NAD


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6295100 mM MES pH 6.0, 150 mM Ammonium sulphate, 15 % w/v PEG4000
Crystal Properties
Matthews coefficientSolvent content
2.7555.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.23α = 90
b = 125.82β = 90
c = 223.9γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42009-10-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-20.933ESRFID14-2

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
12.833.5683.80.1383.838432
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)
12.82.95840.382.43.1

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 SYNTHESISTHROUGHOUT2X582.833.5636256198082.470.211760.209060.26104RANDOM53.699
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]
-0.44-0.270.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.471
r_dihedral_angle_4_deg17.801
r_dihedral_angle_3_deg15.896
r_long_range_B_refined6.066
r_long_range_B_other6.066
r_dihedral_angle_1_deg5.853
r_mcangle_it3.853
r_mcangle_other3.853
r_scangle_it3.46
r_scangle_other3.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.471
r_dihedral_angle_4_deg17.801
r_dihedral_angle_3_deg15.896
r_long_range_B_refined6.066
r_long_range_B_other6.066
r_dihedral_angle_1_deg5.853
r_mcangle_it3.853
r_mcangle_other3.853
r_scangle_it3.46
r_scangle_other3.46
r_mcbond_it2.29
r_mcbond_other2.285
r_scbond_it1.992
r_scbond_other1.991
r_angle_refined_deg1.311
r_angle_other_deg0.928
r_symmetry_vdw_other0.268
r_symmetry_hbond_refined0.196
r_symmetry_vdw_refined0.187
r_nbd_refined0.174
r_nbtor_refined0.162
r_nbd_other0.136
r_xyhbond_nbd_refined0.115
r_nbtor_other0.072
r_chiral_restr0.069
r_ncsr_local_group_10.057
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11092
Nucleic Acid Atoms
Solvent Atoms96
Heterogen Atoms228

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing