3LV2

Crystal structure of Mycobacterium tuberculosis 7,8-diaminopelargonic acid synthase in complex with substrate analog sinefungin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3BV0PDB ENTRY 3BV0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.529120% PEGMME 5000, 0.1M bistris buffer, pH 7.5, VAPOR DIFFUSION, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.141.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.627α = 90
b = 83.43β = 90
c = 157.988γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120IMAGE PLATERIGAKU RAXIS IV++MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.541

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
12.185098.70.07433.412.543477
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)
2.182.395.70.36712.3

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3BV02.183541263219898.690.181190.178550.2322RANDOM27.27
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]
-0.90.96-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.061
r_dihedral_angle_3_deg15.801
r_dihedral_angle_4_deg14.658
r_scangle_it6.06
r_dihedral_angle_1_deg5.87
r_scbond_it4.653
r_mcangle_it3.238
r_mcbond_it2.274
r_angle_refined_deg1.213
r_nbtor_refined0.316
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.061
r_dihedral_angle_3_deg15.801
r_dihedral_angle_4_deg14.658
r_scangle_it6.06
r_dihedral_angle_1_deg5.87
r_scbond_it4.653
r_mcangle_it3.238
r_mcbond_it2.274
r_angle_refined_deg1.213
r_nbtor_refined0.316
r_nbd_refined0.232
r_symmetry_vdw_refined0.204
r_xyhbond_nbd_refined0.179
r_symmetry_hbond_refined0.111
r_chiral_restr0.08
r_bond_refined_d0.009
r_gen_planes_refined0.004
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 Atoms6247
Nucleic Acid Atoms
Solvent Atoms305
Heterogen Atoms57

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling