3GO6 | pdb_00003go6

Crystal Structure of M. tuberculosis ribokinase (Rv2436) in complex with ribose and AMP-PNP

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
3.11	60.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.424	α = 90
b = 117.9	β = 113.93
c = 91.571	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.	2008-07-30	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	1.98	48.17	99.8	0.039	29.146	3.8		52512

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)
	1.98	2.05	100		0.139		3.8	5249

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	MOLECULAR REPLACEMENT	THROUGHOUT	1.98	48.17	52460	2674	99.64	0.172	0.17	0.1725	0.203	0.2059	RANDOM	25.245

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]
-0.27		0.8	0.41		0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.606
r_dihedral_angle_4_deg	16.434
r_dihedral_angle_3_deg	11.649
r_dihedral_angle_1_deg	5.681
r_scangle_it	3.69
r_scbond_it	2.173
r_mcangle_it	1.45
r_angle_refined_deg	1.3
r_mcbond_it	0.855
r_nbtor_refined	0.295
r_nbd_refined	0.194
r_symmetry_vdw_refined	0.188
r_symmetry_hbond_refined	0.141
r_xyhbond_nbd_refined	0.134
r_chiral_restr	0.084
r_bond_refined_d	0.012
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4010
Nucleic Acid Atoms
Solvent Atoms	507
Heterogen Atoms	39

Software

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