6Z5F

CRYSTAL STRUCTURE OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE-1 (RPMFE1) COMPLEXED WITH 3-KETODECANOYL-COA 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 DROP6295100mM MES, pH 6; 15%w/v PEG 4000; 150.91mM ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.856.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.155α = 90
b = 125.977β = 90
c = 223.527γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2020-02-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9762DiamondI03

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
12.2562.631000.0990.0420.9978.46.458828551.3
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)
12.252.291.3880.5870.6711.2

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 REPLACEMENTFREE R-VALUE5OMO2.2562.6388189442899.9310.2110.20930.246470
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]
-1.7112.337-0.626
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.62
r_dihedral_angle_4_deg19.46
r_dihedral_angle_3_deg18.171
r_lrange_it7.525
r_dihedral_angle_1_deg6.293
r_scangle_it2.947
r_mcangle_it2.085
r_scbond_it1.794
r_mcbond_it1.226
r_angle_refined_deg1.205
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.62
r_dihedral_angle_4_deg19.46
r_dihedral_angle_3_deg18.171
r_lrange_it7.525
r_dihedral_angle_1_deg6.293
r_scangle_it2.947
r_mcangle_it2.085
r_scbond_it1.794
r_mcbond_it1.226
r_angle_refined_deg1.205
r_nbtor_refined0.31
r_symmetry_xyhbond_nbd_refined0.251
r_nbd_refined0.219
r_symmetry_nbd_refined0.203
r_xyhbond_nbd_refined0.131
r_chiral_restr0.1
r_bond_refined_d0.005
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11006
Nucleic Acid Atoms
Solvent Atoms163
Heterogen Atoms290

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
REFMACphasing