3BV0

Crystal Structure of PLP Bound 7,8-Diaminopelargonic Acid Synthase in Mycobacterium Tuberculosis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1QJ5PDB entry 1QJ5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7291PEG 8000, 0.1M Tris buffer, 0.1M MgCl2, pH 7.0, VAPOR DIFFUSION, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.346.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.047α = 90
b = 66.47β = 90
c = 203.377γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEOTHER1.541

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
12.213592.90.07321.36.240606
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)
12.212.3378.40.313.53.6

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 1QJ52.213538542206092.640.189530.186980.23814RANDOM22.445
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]
-0.53-0.170.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.877
r_dihedral_angle_4_deg17.42
r_dihedral_angle_3_deg15.473
r_scangle_it6.304
r_dihedral_angle_1_deg5.468
r_scbond_it4.87
r_mcangle_it3.407
r_mcbond_it2.321
r_angle_refined_deg1.181
r_nbtor_refined0.314
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.877
r_dihedral_angle_4_deg17.42
r_dihedral_angle_3_deg15.473
r_scangle_it6.304
r_dihedral_angle_1_deg5.468
r_scbond_it4.87
r_mcangle_it3.407
r_mcbond_it2.321
r_angle_refined_deg1.181
r_nbtor_refined0.314
r_nbd_refined0.222
r_symmetry_vdw_refined0.19
r_xyhbond_nbd_refined0.179
r_symmetry_hbond_refined0.169
r_chiral_restr0.084
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 Atoms6180
Nucleic Acid Atoms
Solvent Atoms245
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing