3HL3 | pdb_00003hl3

2.76 Angstrom Crystal Structure of a Putative Glucose-1-Phosphate Thymidylyltransferase from Bacillus anthracis in Complex with a Sucrose.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MC3	PDB ENTRY 1MC3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	295	Protein Solution: 7.6 mg/mL, 0.25M NaCl, 0.01M Tris-HCl, pH 8.3. Screen: Classics II, drop B10, 0.8M Succinic acid, pH 7.0 Freezing solution: 25% Sucrose, 0.4M Succinic acid, pH 7.0., VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.67	66.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 134.425	α = 90
b = 134.425	β = 90
c = 85.274	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 225 mm CCD	Beryllium lenses	2009-04-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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	2.75	30	99.9	0.089	23.9	10	12153	12153		-3	71.8

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	2.75	2.8	100		0.537	4.9	10.2	601

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 1MC3	2.76	29.1	11573	11573	580	99.75	0.17457	0.17457	0.17302	0.18	0.20573	0.22	RANDOM	30.525

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]
0.32	0.16		0.32		-0.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.918
r_dihedral_angle_4_deg	17.468
r_dihedral_angle_3_deg	10.326
r_scangle_it	4.476
r_dihedral_angle_1_deg	2.84
r_scbond_it	2.753
r_mcangle_it	1.647
r_angle_refined_deg	1.546
r_mcbond_it	0.821
r_angle_other_deg	0.765

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.918
r_dihedral_angle_4_deg	17.468
r_dihedral_angle_3_deg	10.326
r_scangle_it	4.476
r_dihedral_angle_1_deg	2.84
r_scbond_it	2.753
r_mcangle_it	1.647
r_angle_refined_deg	1.546
r_mcbond_it	0.821
r_angle_other_deg	0.765
r_mcbond_other	0.173
r_chiral_restr	0.074
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1943
Nucleic Acid Atoms
Solvent Atoms	37
Heterogen Atoms	23

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	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.