1YXM

Crystal structure of peroxisomal trans 2-enoyl CoA reductase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VL8	PDB entry 1VL8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	294	Ammonium sulphate, Sodium chloride, Sodium cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.2	43.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.152	α = 90
b = 119.014	β = 90
c = 119.909	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		2005-01-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.11	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.9	47.35	98.3	0.046	42	10	88511	88511			33

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.9	2.06	96.9		0.445	3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1VL8	1.9	47	81985	81985	4302	97.49	0.20621	0.20621	0.20417	0.24459	RANDOM	33.504

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]
-0.02					0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.773
r_dihedral_angle_3_deg	13.487
r_dihedral_angle_1_deg	12.739
r_dihedral_angle_4_deg	11.128
r_scangle_it	3.659
r_scbond_it	2.531
r_angle_refined_deg	1.676
r_mcangle_it	1.648
r_mcbond_it	1.006
r_angle_other_deg	0.879
r_mcbond_other	0.422
r_symmetry_hbond_refined	0.349
r_nbd_refined	0.217
r_nbtor_refined	0.183
r_nbd_other	0.18
r_xyhbond_nbd_refined	0.173
r_symmetry_vdw_other	0.172
r_symmetry_vdw_refined	0.169
r_chiral_restr	0.106
r_nbtor_other	0.089
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8288
Nucleic Acid Atoms
Solvent Atoms	374
Heterogen Atoms	35

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing