3TK1

Crystal structure of a MeaB and Rv1496 ortholog from Mycobacterium thermoresistible bound to GDP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3MD0	PDB ENTRY 3MD0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	289	MythA.00200.a.A1 PS00590 at 42.4 mg/mL with 2 mM GDP against PACT screen condition B10, 0.2 M MgCl2, 0.1 M MES pH 6.0, 20% PEG 6000 with 25% ethylene glycol as cryo-protectant, crystal tracking ID 215739b10, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.38	α = 90
b = 106.43	β = 90
c = 134.04	γ = 90

Symmetry
Space Group	P 21 21 21

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	ADSC QUANTUM 315r		2010-07-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.9774	ALS	5.0.1

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	2.4	50	94.8	0.078	17.07	5.3	24555	23270		-3	44.319

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	2.4	2.46	97.8		0.519	3.02

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 3MD0	2.4	50	23269	2369	94.76	0.2296	0.2243	0.2773	RANDOM	37.3745

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]
0.35			-1.06		0.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.103
r_dihedral_angle_4_deg	19.92
r_dihedral_angle_3_deg	16.513
r_dihedral_angle_1_deg	5.519
r_angle_refined_deg	1.492
r_angle_other_deg	1.176
r_chiral_restr	0.071
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.103
r_dihedral_angle_4_deg	19.92
r_dihedral_angle_3_deg	16.513
r_dihedral_angle_1_deg	5.519
r_angle_refined_deg	1.492
r_angle_other_deg	1.176
r_chiral_restr	0.071
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.004
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4435
Nucleic Acid Atoms
Solvent Atoms	107
Heterogen Atoms	57

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.