1SXV | pdb_00001sxv

1.3A Crystal structure of rv3628, Mycobacterium tuberculosis inorganic pyrophosphatase (PPase) at pH5.0

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2PRD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	293	1.7 M ammonium sulphate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.49	64.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.46	α = 90
b = 98.46	β = 90
c = 97.353	γ = 120

Symmetry
Space Group	P 63 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	120	CCD	ADSC QUANTUM 4	mirrors	2004-03-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.93400	ESRF	ID14-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.3	84.5	99.2	0.063	0.063	32	8.2	68651	68086	2	2	14.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.3	1.32	98.2		0.683	0.683	3.15	7.2	3296

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	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	2PRD	1.3	84.5	2	64618	64618	3444	99.17	0.15514	0.15514	0.15437	0.15	0.16945	0.17	RANDOM	14.899

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]
0.63	0.32		0.63		-0.95

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	10.535
r_dihedral_angle_1_deg	6.303
r_sphericity_bonded	5.343
r_scangle_it	3.915
r_scbond_it	2.687
r_mcangle_it	2.043
r_angle_refined_deg	1.667
r_mcbond_it	1.396
r_angle_other_deg	1.077
r_rigid_bond_restr	0.811
r_symmetry_vdw_other	0.333
r_nbd_other	0.26
r_nbd_refined	0.225
r_xyhbond_nbd_refined	0.144
r_symmetry_hbond_refined	0.121
r_chiral_restr	0.097
r_nbtor_other	0.088
r_symmetry_vdw_refined	0.065
r_bond_refined_d	0.013
r_gen_planes_other	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1276
Nucleic Acid Atoms
Solvent Atoms	238
Heterogen Atoms	23

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing