3C90

The 1.25 A Resolution Structure of Phosphoribosyl-ATP Pyrophosphohydrolase from Mycobacterium tuberculosis, crystal form II

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	1M Sodium formate, 0.1M Sodium iodide, 0.1 mM Calcium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.702	α = 90
b = 43.119	β = 96.43
c = 67.547	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	IMAGE PLATE	MAC Science DIP-2030	Osmic optics		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	MACSCIENCE	1.54178

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.79	50	98.9				31912

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1Y6X	1.79	33.56	31690	1605	99.28	0.209	0.207	0.256	RANDOM	27.448

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]
0.18		-0.25	0.81		-1.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.996
r_dihedral_angle_4_deg	15.784
r_dihedral_angle_3_deg	15.282
r_dihedral_angle_1_deg	5.099
r_scangle_it	3.274
r_scbond_it	2
r_mcangle_it	1.227
r_angle_refined_deg	1.152
r_mcbond_it	0.761
r_symmetry_hbond_refined	0.478

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.996
r_dihedral_angle_4_deg	15.784
r_dihedral_angle_3_deg	15.282
r_dihedral_angle_1_deg	5.099
r_scangle_it	3.274
r_scbond_it	2
r_mcangle_it	1.227
r_angle_refined_deg	1.152
r_mcbond_it	0.761
r_symmetry_hbond_refined	0.478
r_symmetry_vdw_refined	0.241
r_nbd_refined	0.215
r_xyhbond_nbd_refined	0.202
r_chiral_restr	0.078
r_metal_ion_refined	0.066
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2708
Nucleic Acid Atoms
Solvent Atoms	233
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
NONIUS/MACSCIENCE	data collection
DENZO	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 R01GM133198.