4HO5 | pdb_00004ho5

Crystal structure of glucose 1-phosphate thymidylyltransferase from Aneurinibacillus thermoaerophilus complexed with TDP-glucose

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.2	293	0.1M sodium cacodylate, 2.0M lithium sulfate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.81	56.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.302	α = 90
b = 90.56	β = 124.96
c = 87.519	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	ADSC QUANTUM 315r	mirrors	2012-03-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL13B1	1.0000	NSRRC	BL13B1

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	1.7	30	99.4	0.049	21.3	4.9		79524

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	1.7	1.76	99.9		0.294		5	7936

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	PDB entry 1H5R	THROUGHOUT	1.7	30	79472	3994	99.1	0.1935	0.192	0.1914	0.2234	0.2233	RANDOM	28.9319

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		-1.73	0.92		-1.91

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.106
r_dihedral_angle_4_deg	18.327
r_dihedral_angle_3_deg	14.706
r_dihedral_angle_1_deg	7.076
r_scangle_it	6.398
r_scbond_it	4.051
r_mcangle_it	2.712
r_mcbond_it	1.7
r_angle_refined_deg	1.455
r_chiral_restr	0.122

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.106
r_dihedral_angle_4_deg	18.327
r_dihedral_angle_3_deg	14.706
r_dihedral_angle_1_deg	7.076
r_scangle_it	6.398
r_scbond_it	4.051
r_mcangle_it	2.712
r_mcbond_it	1.7
r_angle_refined_deg	1.455
r_chiral_restr	0.122
r_bond_refined_d	0.019
r_gen_planes_refined	0.017

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4518
Nucleic Acid Atoms
Solvent Atoms	504
Heterogen Atoms	169

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
MOLREP	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.