6ZIB | pdb_00006zib

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

X-RAY DIFFRACTION

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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	MES, pH 6; 16%w/v PEG 4000; 150mM ammonium sulfate. Co-crystallized with 2mM CoA

Crystal Properties
Matthews coefficient	Solvent content
2.93	57.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.937	α = 90
b = 127.39	β = 90
c = 228.173	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	2.7	48.88	95.5	0.157	0.06	0.995	11.7	7.77		51199			52.6

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	2.7	2.78			1.092	0.406	0.691	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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5OMO	2.7	48.88	50871	2540	94.554	0.234	0.2316	0.23	0.2733	0.27	72.958

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]
6.068			-1.042		-5.026

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.071
r_dihedral_angle_4_deg	20.304
r_dihedral_angle_3_deg	17.798
r_lrange_it	7.179
r_dihedral_angle_1_deg	6.068
r_scangle_it	1.156
r_mcangle_it	1.086
r_angle_refined_deg	1.081
r_scbond_it	0.666
r_mcbond_it	0.582
r_nbtor_refined	0.307
r_symmetry_nbd_refined	0.246
r_nbd_refined	0.208
r_symmetry_xyhbond_nbd_refined	0.187
r_xyhbond_nbd_refined	0.13
r_ncsr_local_group_1	0.097
r_chiral_restr	0.095
r_bond_refined_d	0.004
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11074
Nucleic Acid Atoms
Solvent Atoms	67
Heterogen Atoms	206

Software

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