3HPZ

Crystal structure of Mycobacterium tuberculosis LeuA complexed with bromopyruvate


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
2.0439.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.244α = 90
b = 154.849β = 98.23
c = 68.967γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110IMAGE PLATEMAR scanner 345 mm plateOsmic2007-05-15MSINGLE 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
12.25098.60.11813.13.75620056200
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)
12.22.2887.60.5872.24981

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 3HPS2.243.645329253292287298.590.186820.186820.18330.25169RANDOM29.814
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]
0.020.99-1.031.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.557
r_dihedral_angle_4_deg16.206
r_dihedral_angle_3_deg15.399
r_dihedral_angle_1_deg6.936
r_scangle_it3.794
r_scbond_it2.448
r_angle_refined_deg1.766
r_mcangle_it1.507
r_mcbond_it0.902
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.557
r_dihedral_angle_4_deg16.206
r_dihedral_angle_3_deg15.399
r_dihedral_angle_1_deg6.936
r_scangle_it3.794
r_scbond_it2.448
r_angle_refined_deg1.766
r_mcangle_it1.507
r_mcbond_it0.902
r_nbtor_refined0.303
r_symmetry_hbond_refined0.257
r_symmetry_vdw_refined0.224
r_nbd_refined0.206
r_xyhbond_nbd_refined0.157
r_chiral_restr0.11
r_bond_refined_d0.019
r_gen_planes_refined0.007
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 Atoms8593
Nucleic Acid Atoms
Solvent Atoms448
Heterogen Atoms23

Software

Software
Software NamePurpose
MAR345dtbdata collection
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing