5OMO | pdb_00005omo

CRYSTAL STRUCTURE OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE-1 (RPMFE1) COMPLEXED WITH WITH 3S-HYDROXY-DECANOYL-COA AND 3-KETO-DECANOYL-COA

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	100MM MES PH 6.0, 150MM AMMONIUM SULPHATE, 15% W/V PEG4000

Crystal Properties
Matthews coefficient	Solvent content
2.81	56.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.96	α = 90
b = 125.08	β = 90
c = 223.53	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 315r		2010-11-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.93928	ESRF	ID14-4

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	2.49	47.9	99.2	0.06	0.029	16.6	4.4		64401

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.49	2.62	96.1		0.28	0.158	4.2	4

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	2X58	2.49	47.9	60931	3208	98.73	0.19446	0.19271	0.2	0.22831	0.23	RANDOM	53.337

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]
-0.38			-2.45		2.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.622
r_dihedral_angle_4_deg	18.859
r_dihedral_angle_3_deg	16.153
r_dihedral_angle_1_deg	5.924
r_long_range_B_refined	4.673
r_long_range_B_other	4.673
r_scangle_it	2.234
r_scangle_other	2.234
r_mcangle_it	2.186
r_mcangle_other	2.186
r_chiral_restr_other	1.975
r_angle_refined_deg	1.451
r_scbond_it	1.298
r_scbond_other	1.297
r_mcbond_other	1.24
r_mcbond_it	1.239
r_angle_other_deg	1.039
r_nbd_other	0.239
r_symmetry_nbd_refined	0.194
r_nbd_refined	0.191
r_nbtor_refined	0.167
r_symmetry_xyhbond_nbd_refined	0.151
r_symmetry_nbd_other	0.144
r_xyhbond_nbd_refined	0.126
r_ncsr_local_group_1	0.087
r_chiral_restr	0.082
r_symmetry_nbtor_other	0.074
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11076
Nucleic Acid Atoms
Solvent Atoms	282
Heterogen Atoms	228

Software

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