2PR1 | pdb_00002pr1

Crystal structure of the Bacillus subtilis N-acetyltransferase YlbP protein in complex with Coenzyme-A

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	295	0.01M Cobalt chloride, 0.25M Sodium chloride, 0.1M MES, 1.8M Ammonium sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
4.21	70.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 148.572	α = 90
b = 148.572	β = 90
c = 102.29	γ = 120

Symmetry
Space Group	P 63 2 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	CCD	MARMOSAIC 300 mm CCD	K-B pair biomorph mirrors	2007-03-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.97931	APS	23-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	3.2	30	99	0.116	14.3	6.5	11325	11325		-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	3.2	3.31	99.6		0.477	3.9	6.6	1104

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	3.2	30	10209	1101	98.94	0.21934	0.21548	0.2	0.25462	0.24	RANDOM	76.773

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]
1.63	0.82		1.63		-2.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.896
r_dihedral_angle_4_deg	19.488
r_dihedral_angle_3_deg	14.083
r_dihedral_angle_1_deg	4.727
r_scangle_it	3.518
r_scbond_it	2.083
r_angle_refined_deg	1.56
r_mcangle_it	1.305
r_mcbond_it	0.797
r_nbtor_refined	0.316

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.896
r_dihedral_angle_4_deg	19.488
r_dihedral_angle_3_deg	14.083
r_dihedral_angle_1_deg	4.727
r_scangle_it	3.518
r_scbond_it	2.083
r_angle_refined_deg	1.56
r_mcangle_it	1.305
r_mcbond_it	0.797
r_nbtor_refined	0.316
r_nbd_refined	0.217
r_symmetry_vdw_refined	0.212
r_symmetry_hbond_refined	0.191
r_xyhbond_nbd_refined	0.149
r_chiral_restr	0.108
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2541
Nucleic Acid Atoms
Solvent Atoms	23
Heterogen Atoms	154

Software

Software
Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHARP	phasing

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.