4ECM | pdb_00004ecm

2.3 Angstrom Crystal Structure of a Glucose-1-phosphate Thymidylyltransferase from Bacillus anthracis in Complex with Thymidine-5-diphospho-alpha-D-glucose and Pyrophosphate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3HL3	PDB entry 3HL3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	295	Protein: 7.5 mg/mL, 0.5M NaCl, 0.01M Tris-HCl (pH 8.3), 0.001M Thymidine-5-diphospho-alpha-D-glucose. Screen: PACT (H8), 0.2 Sodium Sulfate, 0.1M TRIS propane, 20% (w/v) PEG 33500, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.7	66.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 135.072	α = 90
b = 135.072	β = 90
c = 85.138	γ = 120

Symmetry
Space Group	P 6 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	Beryllium lenses	2012-03-05	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)	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	2.3	30	99.9	0.108	22.9	10.7	20938	20938		-3	32.4

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	2.3	2.34	100		0.533	5.1	10.9	1022

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 (All)	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 3HL3	2.3	29.24	19775	19775	1073	99.92	0.15442	0.15442	0.15271	0.16	0.18588	0.18	RANDOM	24.768

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]
-0.26	-0.13		-0.26		0.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.567
r_dihedral_angle_4_deg	19.929
r_dihedral_angle_3_deg	10.423
r_scangle_it	4.551
r_dihedral_angle_1_deg	3.556
r_scbond_it	3.009
r_mcangle_it	1.93
r_angle_refined_deg	1.526
r_mcbond_it	1.044
r_angle_other_deg	0.85

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.567
r_dihedral_angle_4_deg	19.929
r_dihedral_angle_3_deg	10.423
r_scangle_it	4.551
r_dihedral_angle_1_deg	3.556
r_scbond_it	3.009
r_mcangle_it	1.93
r_angle_refined_deg	1.526
r_mcbond_it	1.044
r_angle_other_deg	0.85
r_mcbond_other	0.285
r_chiral_restr	0.111
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1940
Nucleic Acid Atoms
Solvent Atoms	226
Heterogen Atoms	45

Software

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