6ZIC

CRYSTAL STRUCTURE OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE-1 (RPMFE1) COMPLEXED WITH 3S-HYDROXYBUTANOYL-COA AND NADH


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; 18%w/v PEG 4000; 175mM ammonium. Co-crystallized with 2mM CoA.
Crystal Properties
Matthews coefficientSolvent content
2.8957.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.637α = 90
b = 127.086β = 90
c = 227.1γ = 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
12.265.12299.60.0950.0360.99811.77.589692438.6
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)
12.22.241001.0220.3860.7152.1

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-VALUE5OMO2.265.12196825492599.4760.2020.20030.233855.296
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]
-1.6260.7520.874
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.243
r_dihedral_angle_4_deg19.067
r_dihedral_angle_3_deg17.262
r_lrange_it7.31
r_dihedral_angle_1_deg6.307
r_scangle_it2.028
r_angle_refined_deg1.54
r_scbond_it1.264
r_mcangle_it1.213
r_mcbond_it0.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.243
r_dihedral_angle_4_deg19.067
r_dihedral_angle_3_deg17.262
r_lrange_it7.31
r_dihedral_angle_1_deg6.307
r_scangle_it2.028
r_angle_refined_deg1.54
r_scbond_it1.264
r_mcangle_it1.213
r_mcbond_it0.69
r_nbtor_refined0.312
r_symmetry_xyhbond_nbd_refined0.254
r_symmetry_nbd_refined0.252
r_nbd_refined0.219
r_xyhbond_nbd_refined0.144
r_chiral_restr0.118
r_gen_planes_refined0.008
r_bond_refined_d0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11036
Nucleic Acid Atoms
Solvent Atoms255
Heterogen Atoms248

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
REFMACphasing