2WD9 | pdb_00002wd9

CRYSTAL STRUCTURE OF HUMAN ACYL-COA SYNTHETASE MEDIUM-CHAIN FAMILY MEMBER 2A (L64P MUTATION) IN COMPLEX WITH IBUPROFEN

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3B7W	PDB ENTRY 3B7W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				0.2M AM ACETATE, 0.1M TRIS PH 8.5, 25% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.32	α = 90
b = 98.32	β = 90
c = 381.44	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS	OSMIC	2008-04-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE

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	2.6	38.92	96.7	0.19	10.1	3.9		54507		2

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	2.6	2.67	90		0.47	2.3	3.2

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3B7W	2.6	38.92	54057	2842	96.7	0.236	0.235	0.23	0.255	0.26	RANDOM	13.29

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]
-0.62			-0.62		1.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.707
r_dihedral_angle_4_deg	16.083
r_dihedral_angle_3_deg	15.186
r_dihedral_angle_1_deg	5.772
r_scangle_it	3.515
r_scbond_it	2.395
r_angle_other_deg	2.199
r_mcangle_it	1.396
r_angle_refined_deg	1.232
r_mcbond_it	0.807
r_mcbond_other	0.108
r_chiral_restr	0.065
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12363
Nucleic Acid Atoms
Solvent Atoms	215
Heterogen Atoms	47

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing