3VBI | pdb_00003vbi

Crystal Structure of AntD, an N-acyltransferase from Bacillus cereus in complex with dTDP-4-amino-4,6-dideoxyglucose and Coenzyme A

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		IN-HOUSE MIR MODEL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	298	25% pentaerythritol ethoxylate (3/4 EO/OH), 2% isopropanol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.115	α = 90
b = 71.115	β = 90
c = 138.179	γ = 90

Symmetry
Space Group	P 41

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	Bruker Platinum 135	Montel	2011-05-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.54178

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.8	38.659	90.9	0.062	0.062	11.8	3.7	63508	57751

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.9	78		0.249	0.249	1.6	1.6	7460

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	IN-HOUSE MIR MODEL	1.8	38.659	57719	54826	2893	90.97	0.20049	0.19821	0.2	0.24498	0.24	RANDOM	27.478

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]
0.2			0.2		-0.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.714
r_dihedral_angle_3_deg	18.239
r_dihedral_angle_4_deg	14.597
r_dihedral_angle_1_deg	7.638
r_scangle_it	5.239
r_scbond_it	3.746
r_mcangle_it	2.281
r_angle_refined_deg	2.277
r_mcbond_it	1.406
r_chiral_restr	0.185

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.714
r_dihedral_angle_3_deg	18.239
r_dihedral_angle_4_deg	14.597
r_dihedral_angle_1_deg	7.638
r_scangle_it	5.239
r_scbond_it	3.746
r_mcangle_it	2.281
r_angle_refined_deg	2.277
r_mcbond_it	1.406
r_chiral_restr	0.185
r_bond_refined_d	0.01
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4311
Nucleic Acid Atoms
Solvent Atoms	298
Heterogen Atoms	262

Software

Software
Software Name	Purpose
PROTEUM PLUS	data collection
PHASER	phasing
REFMAC	refinement
SAINT	data reduction
SADABS	data scaling

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.