3MD0

Crystal structure of arginine/ornithine transport system ATPase from Mycobacterium tuberculosis bound to GDP (a RAS-like GTPase superfamily protein)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QM7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.228950% PEG 200, 0.2 M NaCl, 0.1 M Na K phosphate pH 6.2, 22.0 mg/mL protein, 2 mM GDP, crystal tracking ID 207391d3, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.6353.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.53α = 90
b = 187.36β = 90
c = 66.2γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 9442010-03-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
12.4519.9699.40.07220.56.8415339-350.04
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)
12.452.5197.20.5732.74.62

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 REPLACEMENTTHROUGHOUT2qm72.4519.961526878098.960.2130.2110.251RANDOM45.656
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]
1.29-1.08-0.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.611
r_dihedral_angle_4_deg23.123
r_dihedral_angle_3_deg17.826
r_dihedral_angle_1_deg5.363
r_scangle_it4.025
r_scbond_it2.374
r_angle_refined_deg1.556
r_mcangle_it1.497
r_mcbond_it0.794
r_chiral_restr0.092
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.611
r_dihedral_angle_4_deg23.123
r_dihedral_angle_3_deg17.826
r_dihedral_angle_1_deg5.363
r_scangle_it4.025
r_scbond_it2.374
r_angle_refined_deg1.556
r_mcangle_it1.497
r_mcbond_it0.794
r_chiral_restr0.092
r_bond_refined_d0.015
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2214
Nucleic Acid Atoms
Solvent Atoms80
Heterogen Atoms32

Software

Software
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction