1Y6X | pdb_00001y6x

The 1.25 A resolution structure of phosphoribosyl-ATP pyrophosphohydrolase from Mycobacterium tuberculosis

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291	sodium citrate, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

Crystal Properties
Matthews coefficient	Solvent content
2.5	37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.925	α = 90
b = 62.597	β = 90
c = 67.051	γ = 90

Symmetry
Space Group	I 2 2 2

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	ADSC QUANTUM 4		2002-03-02	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-D	1.0037, 0.9802,0.9799, 0.9572	APS	14-BM-D

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	1.1	45.64	100				24294

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.25	45.64	20798	19181	1042	97.24	0.18458	0.18336	0.1926	0.20747	0.2129	RANDOM	11.028

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]
0.41			0.37		-0.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.035
r_dihedral_angle_3_deg	11.368
r_dihedral_angle_4_deg	5.649
r_dihedral_angle_1_deg	4.475
r_scangle_it	2.487
r_sphericity_free	2.132
r_scbond_it	1.74
r_rigid_bond_restr	1.337
r_sphericity_bonded	1.319
r_mcangle_it	1.004
r_angle_refined_deg	0.985
r_mcbond_it	0.786
r_angle_other_deg	0.715
r_symmetry_vdw_other	0.24
r_mcbond_other	0.231
r_nbd_refined	0.22
r_symmetry_vdw_refined	0.19
r_nbtor_refined	0.177
r_nbd_other	0.156
r_xyhbond_nbd_refined	0.124
r_symmetry_hbond_refined	0.094
r_nbtor_other	0.084
r_chiral_restr	0.053
r_bond_refined_d	0.006
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	677
Nucleic Acid Atoms
Solvent Atoms	151
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
SHELXD	phasing
SHELXE	model building