6EDD | pdb_00006edd

Crystal structure of a GNAT Superfamily PA3944 acetyltransferase in complex with CoA (P1 space group)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6EDV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	289	0.3 ul of 10 mg/ml protein incubated with 5mM CoA and 5 mM colistin was mixed with 0.2 ul of the well condition (MCSG suite I condition 11 - 100 mM Tris-HCl pH 7.0, 200 mM calcium acetate, 20% w/v PEG 3000) and equilibrated against well solution in 96 Well 3 drop Crystallization Plate (Swissci).

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.452	α = 81.88
b = 44.175	β = 73.32
c = 60.125	γ = 89.94

Symmetry
Space Group	P 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	Beryllium Lenses	2017-03-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.55	50	96.2	0.053	0.069	0.044	11.7	2.4		49684

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.58	93.5		0.397	0.521	0.335	0.773		2.1

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	6EDV	1.55	34.89	44683	2225	91.54	0.167	0.1656	0.18	0.1935	0.18	RANDOM	19.859

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]
11.34	5.97	2.72	-15.22	-1.77	3.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	23.946
r_dihedral_angle_4_deg	16.49
r_dihedral_angle_3_deg	12.062
r_dihedral_angle_1_deg	6.522
r_angle_other_deg	1.731
r_angle_refined_deg	1.371
r_chiral_restr	0.081
r_gen_planes_other	0.01
r_bond_refined_d	0.008
r_gen_planes_refined	0.007

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	23.946
r_dihedral_angle_4_deg	16.49
r_dihedral_angle_3_deg	12.062
r_dihedral_angle_1_deg	6.522
r_angle_other_deg	1.731
r_angle_refined_deg	1.371
r_chiral_restr	0.081
r_gen_planes_other	0.01
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3036
Nucleic Acid Atoms
Solvent Atoms	476
Heterogen Atoms	130

Software

Software
Software Name	Purpose
HKL-3000	data reduction
HKL-3000	data scaling
SCALEPACK	data scaling
HKL-3000	phasing
MOLREP	phasing
Coot	model building
REFMAC	refinement

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.