3HQ1

Crystal structure of Mycobacterium tuberculosis LeuA complexed with citrate and Mn2+


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3HPSPDB entry 3HPS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.25291Sodium citrate, PEG MME 2000, pH 6.25, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.0540.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.361α = 90
b = 154.803β = 98.04
c = 69.115γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110IMAGE PLATEMAR scanner 345 mm plateOsmic2007-07-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5417

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
11.75094.60.05222.73.3117445117445
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)
11.71.7668.80.3492.38508

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3HPS1.738.69111160111160597494.680.172080.172080.170380.20366RANDOM18.941
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]
0.490.24-0.28-0.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.63
r_dihedral_angle_4_deg14.671
r_dihedral_angle_3_deg12.452
r_dihedral_angle_1_deg5.628
r_scangle_it3.068
r_scbond_it1.95
r_angle_refined_deg1.288
r_mcangle_it1.278
r_mcbond_it0.765
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.63
r_dihedral_angle_4_deg14.671
r_dihedral_angle_3_deg12.452
r_dihedral_angle_1_deg5.628
r_scangle_it3.068
r_scbond_it1.95
r_angle_refined_deg1.288
r_mcangle_it1.278
r_mcbond_it0.765
r_nbtor_refined0.305
r_nbd_refined0.198
r_symmetry_vdw_refined0.176
r_xyhbond_nbd_refined0.13
r_symmetry_hbond_refined0.114
r_chiral_restr0.086
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8694
Nucleic Acid Atoms
Solvent Atoms896
Heterogen Atoms35

Software

Software
Software NamePurpose
MAR345dtbdata collection
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing