6Z5O

CRYSTAL STRUCTURE OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE-1 (RPMFE1) COMPLEXED WITH COENZYME-A AND OXIDISED NICOTINAMIDE ADENINE DINUCLEOTIDE


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5OMO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP629575mM MES, pH 6; 16%w/v PEG 4000; 125mM ammonium sulfate.
Crystal Properties
Matthews coefficientSolvent content
2.447.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.646α = 90
b = 106.664β = 90
c = 114.512γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-08-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.972957ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)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
11.748.995.10.1260.0460.9959.98.138067521.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7394.91.0050.370.8112

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTNONE5OMO1.748.980615419094.770.1910.1890.233225.328
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]
0.7480.844-1.591
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.574
r_dihedral_angle_4_deg17.748
r_dihedral_angle_3_deg14.353
r_lrange_it6.591
r_dihedral_angle_1_deg5.878
r_scangle_it4.335
r_scbond_it2.922
r_mcangle_it2.586
r_mcbond_it1.861
r_angle_refined_deg1.612
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.574
r_dihedral_angle_4_deg17.748
r_dihedral_angle_3_deg14.353
r_lrange_it6.591
r_dihedral_angle_1_deg5.878
r_scangle_it4.335
r_scbond_it2.922
r_mcangle_it2.586
r_mcbond_it1.861
r_angle_refined_deg1.612
r_nbtor_refined0.318
r_symmetry_nbd_refined0.216
r_nbd_refined0.211
r_symmetry_xyhbond_nbd_refined0.181
r_xyhbond_nbd_refined0.151
r_chiral_restr0.118
r_gen_planes_refined0.009
r_bond_refined_d0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5503
Nucleic Acid Atoms
Solvent Atoms667
Heterogen Atoms132

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
REFMACphasing