4QVT | pdb_00004qvt

Crystal structure of predicted N-acyltransferase (ypeA) in complex with acetyl-CoA from Escherichia coli

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	292	0.2 M lithium sulfate, 25% w/v PEG3350, 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.334	α = 90
b = 139.968	β = 112.11
c = 75.358	γ = 90

Symmetry
Space Group	P 1 21 1

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	mirrors	2014-07-04	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	1.948	69.984	98.6	0.073	33.8	4.6	92573	92573		-3	53.2

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	1.948	1.98	95.2		0.46	2.05	3.9	4492

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 3PDO	1.948	69.98	87793	87793	4600	98.06	0.19033	0.18813	0.2	0.23236	0.23	RANDOM	55.082

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]
-0.41		1.17	1.85		-1.8

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.113
r_dihedral_angle_4_deg	13.993
r_dihedral_angle_3_deg	12.218
r_long_range_B_refined	8.399
r_long_range_B_other	8.376
r_scangle_other	6.582
r_scbond_it	4.895
r_scbond_other	4.813
r_mcangle_it	4.027
r_mcangle_other	4.026
r_mcbond_it	3.337
r_mcbond_other	3.278
r_dihedral_angle_1_deg	2.878
r_angle_refined_deg	1.871
r_angle_other_deg	0.832
r_chiral_restr	0.117
r_gen_planes_refined	0.023
r_gen_planes_other	0.018
r_bond_refined_d	0.013
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9140
Nucleic Acid Atoms
Solvent Atoms	243
Heterogen Atoms	458

Software

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