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)
Type	Source	Accession Code	Details
experimental model	PDB	5OMO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	295	100mM MES, pH 6; 15%w/v PEG 4000; 150.91mM ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.155	α = 90
b = 125.977	β = 90
c = 223.527	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		2020-02-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	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	2.25	62.63	100	0.099	0.042	0.997	8.4	6.45		88285			51.3

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)	Redundancy	Number Unique Reflections (All)
1	2.25	2.29			1.388	0.587	0.671	1.2

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	2.25	62.63	88189	4428	99.931	0.211	0.2093	0.2464	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]
-1.711			2.337		-0.626

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.62
r_dihedral_angle_4_deg	19.46
r_dihedral_angle_3_deg	18.171
r_lrange_it	7.525
r_dihedral_angle_1_deg	6.293
r_scangle_it	2.947
r_mcangle_it	2.085
r_scbond_it	1.794
r_mcbond_it	1.226
r_angle_refined_deg	1.205

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.62
r_dihedral_angle_4_deg	19.46
r_dihedral_angle_3_deg	18.171
r_lrange_it	7.525
r_dihedral_angle_1_deg	6.293
r_scangle_it	2.947
r_mcangle_it	2.085
r_scbond_it	1.794
r_mcbond_it	1.226
r_angle_refined_deg	1.205
r_nbtor_refined	0.31
r_symmetry_xyhbond_nbd_refined	0.251
r_nbd_refined	0.219
r_symmetry_nbd_refined	0.203
r_xyhbond_nbd_refined	0.131
r_chiral_restr	0.1
r_bond_refined_d	0.005
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11006
Nucleic Acid Atoms
Solvent Atoms	163
Heterogen Atoms	290

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.