6Z5V

CRYSTAL STRUCTURE OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE-1 (RPMFE1) COMPLEXED WITH 3-KETODECANOYL-COA IN CROTONASE FOLD AND OXIDISED NICOTINAMIDE ADENINE DINUCLEOTIDE IN HAD FOLD


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6295125mM MES, pH 6; 17%w/v PEG4000; 175mM ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.856.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.314α = 90
b = 126.298β = 90
c = 224.9γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2019-10-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

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
12.3229.1599.20.0530.0220.99917.96.668000753.7
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)
12.332.3786.60.7980.3590.6492.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5OMO2.3329.14979923407299.0480.2050.20350.225870
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]
4.177-1.923-2.254
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.409
r_dihedral_angle_4_deg18.441
r_dihedral_angle_3_deg17.064
r_lrange_it9.104
r_dihedral_angle_1_deg6.093
r_scangle_it2.187
r_mcangle_it1.91
r_scbond_it1.379
r_angle_refined_deg1.186
r_mcbond_it1.102
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.409
r_dihedral_angle_4_deg18.441
r_dihedral_angle_3_deg17.064
r_lrange_it9.104
r_dihedral_angle_1_deg6.093
r_scangle_it2.187
r_mcangle_it1.91
r_scbond_it1.379
r_angle_refined_deg1.186
r_mcbond_it1.102
r_nbtor_refined0.308
r_symmetry_xyhbond_nbd_refined0.305
r_symmetry_nbd_refined0.213
r_nbd_refined0.212
r_xyhbond_nbd_refined0.136
r_chiral_restr0.098
r_gen_planes_refined0.006
r_bond_refined_d0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11000
Nucleic Acid Atoms
Solvent Atoms167
Heterogen Atoms234

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
REFMACphasing