3HVU | pdb_00003hvu

1.95 Angstrom Crystal Structure of Complex of Hypoxanthine-Guanine Phosphoribosyltransferase from Bacillus anthracis with 2-(N-morpholino)ethanesulfonic acid (MES)

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	6	295	protein: 7mg/mL, 0.25M NaCl, 0.01M Tris-HCl pH 8.3; screen: PACT D3, 0.1M MMT buffer pH 6.0, 25% v/v PEG 1500, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.713	α = 90
b = 93.377	β = 90.03
c = 94.9	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	Beryllium lenses	2009-05-29	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	1.95	30	98	0.054	21.9	3.8	65972	65972	-3		33.2

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	1.95	1.98	92.5		0.494	2.2	3.3	3069

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	3H83	1.95	29.96	62332	62332	3338	98.07	0.19427	0.19427	0.19227	0.21	0.23172	0.23	RANDOM	22.879

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]
-1.04		-0.3	5.08		-4.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.028
r_dihedral_angle_3_deg	9.141
r_dihedral_angle_4_deg	6.727
r_scangle_it	4.576
r_scbond_it	2.984
r_dihedral_angle_1_deg	2.481
r_mcangle_it	1.834
r_angle_refined_deg	1.644
r_mcbond_it	1.082
r_angle_other_deg	0.881

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.028
r_dihedral_angle_3_deg	9.141
r_dihedral_angle_4_deg	6.727
r_scangle_it	4.576
r_scbond_it	2.984
r_dihedral_angle_1_deg	2.481
r_mcangle_it	1.834
r_angle_refined_deg	1.644
r_mcbond_it	1.082
r_angle_other_deg	0.881
r_mcbond_other	0.321
r_chiral_restr	0.104
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5852
Nucleic Acid Atoms
Solvent Atoms	498
Heterogen Atoms	52

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.