1V8G | pdb_00001v8g

Crystal structure of anthranilate phosphoribosyltransferase (TrpD) from Thermus thermophilus HB8

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	microbach	5.8	291	27.5 w/v PEG4000, 0.1M citrate, pH 5.8, microbach, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.38	47.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 143.318	α = 90
b = 72.45	β = 110.36
c = 73.539	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	100	CCD	RIGAKU JUPITER	mirror	2003-10-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B2	1.00	SPring-8	BL26B2

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	2.1	40	99.9	0.072	0.067	15.2	3.65	41300	41300			19.9

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)
	2.1	2.18	99.9		0.255	0.22	3.17	3.56	3986

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	1KGZ	2.1	40	41300	41300	2034	99.9	0.212	0.212	0.21	0.255	0.22	RANDOM	32.8

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]
-6.09		-5.07	11.06		-4.97

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	21
c_scangle_it	3.02
c_mcangle_it	2.31
c_scbond_it	2.08
c_mcbond_it	1.45
c_angle_deg	1.2
c_improper_angle_d	0.77
c_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4824
Nucleic Acid Atoms
Solvent Atoms	543
Heterogen Atoms

Software

Software
Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	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.