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)
TypeSourceAccession CodeDetails
experimental modelPDB 3MD0PDB ENTRY 3MD0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6289MythA.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 coefficientSolvent content
2.1241.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.38α = 90
b = 106.43β = 90
c = 134.04γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2010-07-21MSINGLE 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
12.45094.80.07817.075.32455523270-344.319
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)
12.42.4697.80.5193.02

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3MD02.45023269236994.760.22960.22430.2773RANDOM37.3745
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]
0.35-1.060.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.103
r_dihedral_angle_4_deg19.92
r_dihedral_angle_3_deg16.513
r_dihedral_angle_1_deg5.519
r_angle_refined_deg1.492
r_angle_other_deg1.176
r_chiral_restr0.071
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.103
r_dihedral_angle_4_deg19.92
r_dihedral_angle_3_deg16.513
r_dihedral_angle_1_deg5.519
r_angle_refined_deg1.492
r_angle_other_deg1.176
r_chiral_restr0.071
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.004
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4435
Nucleic Acid Atoms
Solvent Atoms107
Heterogen Atoms57

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction