3KB8 | pdb_00003kb8

2.09 Angstrom resolution structure of a hypoxanthine-guanine phosphoribosyltransferase (hpt-1) from Bacillus anthracis str. 'Ames Ancestor' in complex with GMP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3H83

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.3	295	The Classics II Suite, condition B6, mixed at 1:1 v/v ratio with the protein at 7.4 mg/mL in 0.5 M NaCl, 5 mM BME, 1 mM GMP, 1 mM MgCl2, 10 mM Tris/HCl pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.22	α = 90
b = 80.477	β = 101.24
c = 120.236	γ = 90

Symmetry
Space Group	P 1 21 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	MARMOSAIC 300 mm CCD	Be Lenses/Diamond Laue Mono	2009-07-22	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	2.09	50	94	0.101	9.61	3.3	56550	56550		-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	2.09	2.13	99.5		0.539	2.66	3	2964

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	3H83	2.09	30.08	53702	53702	2830	93.92	0.20582	0.20385	0.22	0.2431	0.26	RANDOM	24.226

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]
		-2.59	0.33		-1.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.86
r_dihedral_angle_3_deg	10.261
r_dihedral_angle_4_deg	7.432
r_scangle_it	4.359
r_dihedral_angle_1_deg	3.23
r_scbond_it	2.944
r_mcangle_it	1.804
r_angle_refined_deg	1.696
r_mcbond_it	1.032
r_angle_other_deg	0.889

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.86
r_dihedral_angle_3_deg	10.261
r_dihedral_angle_4_deg	7.432
r_scangle_it	4.359
r_dihedral_angle_1_deg	3.23
r_scbond_it	2.944
r_mcangle_it	1.804
r_angle_refined_deg	1.696
r_mcbond_it	1.032
r_angle_other_deg	0.889
r_mcbond_other	0.306
r_chiral_restr	0.104
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5921
Nucleic Acid Atoms
Solvent Atoms	253
Heterogen Atoms	190

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.