3PL1 | pdb_00003pl1

Determination of the crystal structure of the pyrazinamidase from M.tuberculosis : a structure-function analysis for prediction resistance to pyrazinamide.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1IM5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.6	298	1.6M Sulfate de Magnesium, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.1	α = 90
b = 84.1	β = 90
c = 100	γ = 120

Symmetry
Space Group	P 61 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	273	CCD	MARRESEARCH		2008-02-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.97	ESRF	ID23-2

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	2.2	42.3	92.9		11.6		11014

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.2	2.3	72.5		0.498	3.4	11.5	1260

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1IM5	2.2	42.03	10463	551	100	0.19679	0.1945	0.2	0.23996	0.24	RANDOM	45.08

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]
0.25	0.12		0.25		-0.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.041
r_dihedral_angle_4_deg	24.402
r_dihedral_angle_3_deg	15.885
r_dihedral_angle_1_deg	9.182
r_scangle_it	5.698
r_scbond_it	3.829
r_mcangle_it	2.235
r_angle_refined_deg	2.118
r_mcbond_it	1.383
r_nbtor_refined	0.31
r_symmetry_hbond_refined	0.31
r_nbd_refined	0.251
r_xyhbond_nbd_refined	0.199
r_chiral_restr	0.16
r_symmetry_vdw_refined	0.15
r_bond_refined_d	0.026
r_gen_planes_refined	0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1372
Nucleic Acid Atoms
Solvent Atoms	44
Heterogen Atoms	1

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling