4GT1 | pdb_00004gt1

Crystal structure of a MeaB- and MMAA-like GTPase from Mycobacterium tuberculosis bound to 2'-deoxyguanosine diphosphate

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.9	289	MytuD.00200.a.A1 at 22 mg/mL with 4 mM dGTP against 0.1 M NaKHPO4, 48% PEG 200, 0.2 M NaCl, crystal tracking ID 236287b6, unique puck ID aqu7-6, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.92	α = 90
b = 187.82	β = 90
c = 66.46	γ = 90

Symmetry
Space Group	C 2 2 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		2012-08-04	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	50	100	0.048	29.53	8.1	28351	28337		-3	36.499

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	2.05	100		0.465	4.66

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3md0	2	45.45	28336	1431	99.95	0.1908	0.1889	0.2	0.2269	0.23	RANDOM	38.2709

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]
1.97			-1.37		-0.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.771
r_dihedral_angle_4_deg	17.392
r_dihedral_angle_3_deg	12.75
r_dihedral_angle_1_deg	4.994
r_angle_refined_deg	1.514
r_angle_other_deg	0.832
r_chiral_restr	0.086
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.771
r_dihedral_angle_4_deg	17.392
r_dihedral_angle_3_deg	12.75
r_dihedral_angle_1_deg	4.994
r_angle_refined_deg	1.514
r_angle_other_deg	0.832
r_chiral_restr	0.086
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2198
Nucleic Acid Atoms
Solvent Atoms	140
Heterogen Atoms	48

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.