4GT1

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)
TypeSourceAccession CodeDetails
experimental modelPDB 3MD0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.9289MytuD.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 coefficientSolvent content
2.6653.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.92α = 90
b = 187.82β = 90
c = 66.46γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2012-08-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.10.9774ALS5.0.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12501000.04829.538.12835128337-336.499
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.051000.4654.66

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3md0245.4528336143199.950.19080.18890.2269RANDOM38.2709
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.771
r_dihedral_angle_4_deg17.392
r_dihedral_angle_3_deg12.75
r_dihedral_angle_1_deg4.994
r_angle_refined_deg1.514
r_angle_other_deg0.832
r_chiral_restr0.086
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.771
r_dihedral_angle_4_deg17.392
r_dihedral_angle_3_deg12.75
r_dihedral_angle_1_deg4.994
r_angle_refined_deg1.514
r_angle_other_deg0.832
r_chiral_restr0.086
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2198
Nucleic Acid Atoms
Solvent Atoms140
Heterogen Atoms48

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction