3HPX

Crystal structure of Mycobacterium tuberculosis LeuA active site domain 1-425 (truncation mutant delta:426-644)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1SR9PDB entry 1SR9

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
2.0941.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.025α = 62.45
b = 70.886β = 81.41
c = 70.043γ = 70.26
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110IMAGE PLATEMAR scanner 345 mm plateOsmic2005-10-10MSINGLE 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
12.033094.50.12617.77.64706647066
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)
12.032.184.70.4893.84222

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 1SR92.03304467044670239694.50.177160.177160.173810.23794RANDOM18.097
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]
-0.2-0.090.13-0.59-0.751.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.076
r_dihedral_angle_4_deg15.726
r_dihedral_angle_3_deg14.337
r_dihedral_angle_1_deg6.663
r_scangle_it3.739
r_scbond_it2.479
r_angle_refined_deg1.666
r_mcangle_it1.39
r_mcbond_it0.917
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.076
r_dihedral_angle_4_deg15.726
r_dihedral_angle_3_deg14.337
r_dihedral_angle_1_deg6.663
r_scangle_it3.739
r_scbond_it2.479
r_angle_refined_deg1.666
r_mcangle_it1.39
r_mcbond_it0.917
r_nbtor_refined0.303
r_nbd_refined0.201
r_symmetry_vdw_refined0.198
r_xyhbond_nbd_refined0.19
r_symmetry_hbond_refined0.173
r_chiral_restr0.116
r_bond_refined_d0.019
r_gen_planes_refined0.008
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 Atoms6285
Nucleic Acid Atoms
Solvent Atoms633
Heterogen Atoms14

Software

Software
Software NamePurpose
MAR345dtbdata collection
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing