4QUS | pdb_00004qus

1.28 Angstrom resolution crystal structure of predicted acyltransferase with acyl-CoA N-acyltransferase domain (ypeA) from Escherichia coli str. K-12 substr. MG1655

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9	295	7 mg/mL protein (no tag) in 10 mM Tris-HCl, pH 8.3, 500 mM sodium chloride, 5 mM BME, crystallization: the PACT Suite A6 (#6): 0.1 M SPG buffer, pH 9.0, 25% w/v PEG1500, cryo-protection: well solution soak, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.51	51.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.817	α = 90
b = 90.817	β = 90
c = 84.167	γ = 90

Symmetry
Space Group	I 4

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	MARMOSAIC 300 mm CCD	Bimorph K-B pair mirrors	2014-06-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.97910	APS	21-ID-D

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	1.28	30	99.9	0.052	26.25	5	87246	87246		-3

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	1.28	1.3	100		0.619	2.5	4.8

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 (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 2PDO	1.28	28.72	82845	82845	4387	99.74	0.11083	0.10935	0.11	0.13859	0.14	RANDOM	20.899

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]
0.03			0.03		-0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	53.156
r_dihedral_angle_2_deg	31.485
r_dihedral_angle_4_deg	15.249
r_sphericity_bonded	11.864
r_dihedral_angle_3_deg	10.093
r_dihedral_angle_1_deg	4.131
r_rigid_bond_restr	2.143
r_angle_refined_deg	1.643
r_angle_other_deg	0.877
r_chiral_restr	0.101
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2343
Nucleic Acid Atoms
Solvent Atoms	537
Heterogen Atoms	22

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling