5MGB

Crystal Structure of Rat Peroxisomal Multifunctional enzyme Type-1 (RPMFE1) Complexed with Acetoacetyl-CoA and NAD

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2X58

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6	295	100 mM MES pH 6.0, 150 mM Ammonium sulphate, 15 % w/v PEG4000

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.23	α = 90
b = 125.82	β = 90
c = 223.9	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	CCD	ADSC QUANTUM 4		2009-10-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.933	ESRF	ID14-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.8	33.56	83.8	0.13	8	3.8		38432

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.95	84		0.38	2.4	3.1

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	2X58	2.8	33.56	36256	1980	82.47	0.21176	0.20906	0.26104	RANDOM	53.699

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]
-0.44			-0.27		0.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.471
r_dihedral_angle_4_deg	17.801
r_dihedral_angle_3_deg	15.896
r_long_range_B_refined	6.066
r_long_range_B_other	6.066
r_dihedral_angle_1_deg	5.853
r_mcangle_it	3.853
r_mcangle_other	3.853
r_scangle_it	3.46
r_scangle_other	3.46
r_mcbond_it	2.29
r_mcbond_other	2.285
r_scbond_it	1.992
r_scbond_other	1.991
r_angle_refined_deg	1.311
r_angle_other_deg	0.928
r_symmetry_vdw_other	0.268
r_symmetry_hbond_refined	0.196
r_symmetry_vdw_refined	0.187
r_nbd_refined	0.174
r_nbtor_refined	0.162
r_nbd_other	0.136
r_xyhbond_nbd_refined	0.115
r_nbtor_other	0.072
r_chiral_restr	0.069
r_ncsr_local_group_1	0.057
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11092
Nucleic Acid Atoms
Solvent Atoms	96
Heterogen Atoms	228

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
REFMAC	phasing