3GO7 | pdb_00003go7

Crystal Structure of M. tuberculosis ribokinase (Rv2436) in complex with ribose

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	295	0.2 M Sodium/potassium phosphate, 0.1 M Bis-Tris propane, 16% PEG 3350, pH 6.5, vapor diffusion, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.08	60.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.025	α = 90
b = 119.207	β = 115
c = 89.768	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	100	CCD	MARMOSAIC 225 mm CCD	Rosenbaum-Rock monochromator high-resolution double-crystal Si (111) sagittal focusing. Rosenbaum-Rock vertical focusing mirror.	2008-10-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	1.00	APS	22-BM

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	2.5	50	99.1	0.063	19.959	3.6		26190

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)
	2.5	2.54	89.6		0.438		2.2	1171

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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		THROUGHOUT	2.5	42.22	25905	1308	99.19	0.179	0.176	0.1779	0.237	0.2322	RANDOM	45.245

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]
1.47		0.1	-0.18		-1.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.787
r_dihedral_angle_4_deg	20.038
r_dihedral_angle_3_deg	15.918
r_dihedral_angle_1_deg	6.357
r_scangle_it	3.32
r_scbond_it	1.954
r_mcangle_it	1.457
r_angle_refined_deg	1.399
r_mcbond_it	0.816
r_nbtor_refined	0.305
r_symmetry_hbond_refined	0.23
r_nbd_refined	0.213
r_symmetry_vdw_refined	0.166
r_xyhbond_nbd_refined	0.16
r_chiral_restr	0.084
r_bond_refined_d	0.013
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4010
Nucleic Acid Atoms
Solvent Atoms	229
Heterogen Atoms	12

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling