3NXS

Crystal structure of LAO/AO transport system from Mycobacterium smegmatis bound to GDP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3MD0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP9289JCSG+ condition F6, 0.1% Bicine pH 9.0, 10% MPD as crystallant, 28.66 mg/mL protein, crystal tracking ID 215415f6, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.9157.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.63α = 90
b = 91.46β = 90
c = 57.47γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2010-06-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.21.0ALS5.0.2

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
12.35098.20.05422.878.71900818658-352.616
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)
12.32.3697.90.4894.3

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 REPLACEMENTTHROUGHOUT3MD02.3501858294397.750.20980.20860.2312RANDOM56.8727
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]
-3.131.181.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.045
r_dihedral_angle_4_deg22.532
r_dihedral_angle_3_deg15.167
r_dihedral_angle_1_deg5.956
r_scangle_it4.418
r_scbond_it2.658
r_mcangle_it1.757
r_angle_refined_deg1.501
r_mcbond_it0.931
r_chiral_restr0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.045
r_dihedral_angle_4_deg22.532
r_dihedral_angle_3_deg15.167
r_dihedral_angle_1_deg5.956
r_scangle_it4.418
r_scbond_it2.658
r_mcangle_it1.757
r_angle_refined_deg1.501
r_mcbond_it0.931
r_chiral_restr0.1
r_bond_refined_d0.015
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2283
Nucleic Acid Atoms
Solvent Atoms90
Heterogen Atoms29

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction