6ZIC | pdb_00006zic

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)
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; 18%w/v PEG 4000; 175mM ammonium. Co-crystallized with 2mM CoA.

Crystal Properties
Matthews coefficient	Solvent content
2.89	57.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.637	α = 90
b = 127.086	β = 90
c = 227.1	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 PILATUS 6M		2018-08-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.972957	ESRF	ID23-1

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.2	65.122	99.6	0.095	0.036	0.998	11.7	7.58		96924			38.6

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)	Redundancy	Number Unique Reflections (All)
1	2.2	2.24	100		1.022	0.386	0.715	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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5OMO	2.2	65.121	96825	4925	99.476	0.202	0.2003	0.2	0.2338	0.24	55.296

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]
-1.626			0.752		0.874

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.243
r_dihedral_angle_4_deg	19.067
r_dihedral_angle_3_deg	17.262
r_lrange_it	7.31
r_dihedral_angle_1_deg	6.307
r_scangle_it	2.028
r_angle_refined_deg	1.54
r_scbond_it	1.264
r_mcangle_it	1.213
r_mcbond_it	0.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.243
r_dihedral_angle_4_deg	19.067
r_dihedral_angle_3_deg	17.262
r_lrange_it	7.31
r_dihedral_angle_1_deg	6.307
r_scangle_it	2.028
r_angle_refined_deg	1.54
r_scbond_it	1.264
r_mcangle_it	1.213
r_mcbond_it	0.69
r_nbtor_refined	0.312
r_symmetry_xyhbond_nbd_refined	0.254
r_symmetry_nbd_refined	0.252
r_nbd_refined	0.219
r_xyhbond_nbd_refined	0.144
r_chiral_restr	0.118
r_gen_planes_refined	0.008
r_bond_refined_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11036
Nucleic Acid Atoms
Solvent Atoms	255
Heterogen Atoms	248

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.