2Y88

CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS PHOSPHORIBOSYL ISOMERASE (VARIANT D11N) WITH BOUND PRFAR

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Y85	PDB ENTRY 2Y85

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				0.1M HEPES PH7.5, 1.4M TRI-SODIUM CITRATE

Crystal Properties
Matthews coefficient	Solvent content
2.56	52.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.27	α = 90
b = 63.27	β = 90
c = 131.22	γ = 90

Symmetry
Space Group	P 43 21 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	MARRESEARCH		2006-02-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13		EMBL/DESY, HAMBURG	X13

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	1.33	20	99.1	0.04	0.58	8.4		61458		-3	16.9

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	1.33	1.4	95.8		0.58	3.4	7.4

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 2Y85	1.33	56.98	58387	3082	99.709	0.14	0.1379	0.1836	RANDOM	14.109

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]
0.109			0.109		-0.218

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.422
r_dihedral_angle_4_deg	19.898
r_dihedral_angle_3_deg	11.95
r_scangle_it	7.261
r_dihedral_angle_1_deg	6.24
r_scbond_it	6.054
r_mcangle_it	5.129
r_mcbond_it	4.75
r_angle_refined_deg	2.206
r_angle_other_deg	1.183
r_symmetry_vdw_other	0.344
r_nbd_refined	0.242
r_nbd_other	0.236
r_xyhbond_nbd_refined	0.197
r_symmetry_hbond_refined	0.195
r_nbtor_refined	0.191
r_symmetry_vdw_refined	0.187
r_chiral_restr	0.161
r_nbtor_other	0.116
r_bond_refined_d	0.025
r_gen_planes_refined	0.011
r_bond_other_d	0.003
r_gen_planes_other	0.002
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1804
Nucleic Acid Atoms
Solvent Atoms	394
Heterogen Atoms	37

Software

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