2VVO

Crystal structure of Mycobacterium tuberculosis ribose-5-phosphate isomerase B in complex with alpha d-allose 6-phosphate

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				1M TRI-NA CITRATE, 0.1M NA CACODYLATE PH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.46	50

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 152.744	α = 90
b = 92.501	β = 98.92
c = 60.967	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	110	CCD	ADSC CCD		2006-03-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4		ESRF	ID14-4

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	1.85	60.19	91.7	0.07	12.8	4.2		65360		2.6	23.4

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	1.85	1.95	61.8		0.51	2.6	4.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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 1USL	1.85	40	2.6	62048	3307	91.5	0.162	0.16	0.196	RANDOM	18.56

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]
-0.57		-0.17	-0.39		0.91

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.274
r_dihedral_angle_4_deg	17.016
r_dihedral_angle_3_deg	13.148
r_dihedral_angle_1_deg	6.043
r_scangle_it	3.675
r_scbond_it	2.463
r_angle_refined_deg	1.441
r_mcangle_it	1.361
r_mcbond_it	1.082
r_angle_other_deg	1.002
r_symmetry_vdw_other	0.323
r_nbd_refined	0.209
r_nbd_other	0.205
r_nbtor_refined	0.168
r_xyhbond_nbd_refined	0.133
r_symmetry_hbond_refined	0.132
r_chiral_restr	0.088
r_nbtor_other	0.086
r_symmetry_vdw_refined	0.082
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
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	5897
Nucleic Acid Atoms
Solvent Atoms	420
Heterogen Atoms	80

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
REFMAC	phasing