4QYI | pdb_00004qyi

1.95 Angstrom resolution crystal structure of a hypoxanthine-guanine phosphoribosyltransferase (hpt-2) from Bacillus anthracis str. 'Ames Ancestor' with HEPES molecule in the active site

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3O7M	pdb entry 3O7M

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	295	protein: 7 mg/mL in 10 mM Tris-HCl pH 8.3, 500 mM NaCl, 5 mM BME crystallization: The PACT Suite C10 (#34): 0.2 M MgCl2, 0.1 M HEPES pH 7.0, 20% (w/v) PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 172.779	α = 90
b = 117.009	β = 90.96
c = 56.883	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	MARMOSAIC 225 mm CCD	Be lenses	2011-06-29	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	1.95	30	98.4	0.058	19.1	3.6	81640	81640		-3	33

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	85.5		0.386	2.1	2.4	3512

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	pdb entry 3O7M	1.95	27.99	76977	76977	4060	98.53	0.22288	0.22135	0.2247	0.25243	0.2567	RANDOM	55.655

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]
-4.81		-3.35	1.96		2.9

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.829
r_dihedral_angle_3_deg	9.672
r_dihedral_angle_4_deg	9.666
r_dihedral_angle_1_deg	2.671
r_angle_refined_deg	1.803
r_angle_other_deg	1.145
r_chiral_restr	0.099
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_bond_other_d	0.006
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6803
Nucleic Acid Atoms
Solvent Atoms	370
Heterogen Atoms	100

Software

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