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)
Type	Source	Accession Code	Details
experimental model	PDB	5OMO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	295	125mM MES, pH 6; 17%w/v PEG4000; 175mM ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.6

Crystal Data

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

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER2 X 16M		2019-10-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.32	29.15	99.2	0.053	0.022	0.999	17.9	6.66		80007			53.7

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)	Redundancy	Number Unique Reflections (All)
1	2.33	2.37	86.6		0.798	0.359	0.649	2.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5OMO	2.33	29.149	79923	4072	99.048	0.205	0.2035	0.2258	70

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
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.409
r_dihedral_angle_4_deg	18.441
r_dihedral_angle_3_deg	17.064
r_lrange_it	9.104
r_dihedral_angle_1_deg	6.093
r_scangle_it	2.187
r_mcangle_it	1.91
r_scbond_it	1.379
r_angle_refined_deg	1.186
r_mcbond_it	1.102

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.409
r_dihedral_angle_4_deg	18.441
r_dihedral_angle_3_deg	17.064
r_lrange_it	9.104
r_dihedral_angle_1_deg	6.093
r_scangle_it	2.187
r_mcangle_it	1.91
r_scbond_it	1.379
r_angle_refined_deg	1.186
r_mcbond_it	1.102
r_nbtor_refined	0.308
r_symmetry_xyhbond_nbd_refined	0.305
r_symmetry_nbd_refined	0.213
r_nbd_refined	0.212
r_xyhbond_nbd_refined	0.136
r_chiral_restr	0.098
r_gen_planes_refined	0.006
r_bond_refined_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11000
Nucleic Acid Atoms
Solvent Atoms	167
Heterogen Atoms	234

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
REFMAC	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.