2WGD

Crystal structure of KasA of Mycobacterium tuberculosis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GP6PDB ENTRY 2GP6

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
12-PROPANOL, NACL HEPES PH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.9658.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.529α = 90
b = 77.529β = 90
c = 146.803γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100RIGAKU IMAGING PLATEMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF

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
12.0139.5599.70.0894.43460725.4
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)
12.012.081000.3434.3

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 2GP62.0138.77834601173499.5940.1810.17980.2143RANDOM32.865
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]
0.9470.4740.947-1.421
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.678
r_dihedral_angle_4_deg16.801
r_dihedral_angle_3_deg11.889
r_dihedral_angle_1_deg5.959
r_scangle_it3.264
r_scbond_it1.952
r_angle_refined_deg1.296
r_mcangle_it1.245
r_mcbond_it0.666
r_symmetry_vdw_other0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.678
r_dihedral_angle_4_deg16.801
r_dihedral_angle_3_deg11.889
r_dihedral_angle_1_deg5.959
r_scangle_it3.264
r_scbond_it1.952
r_angle_refined_deg1.296
r_mcangle_it1.245
r_mcbond_it0.666
r_symmetry_vdw_other0.304
r_nbd_refined0.219
r_nbtor_refined0.17
r_symmetry_hbond_refined0.139
r_mcbond_other0.138
r_xyhbond_nbd_refined0.127
r_symmetry_vdw_refined0.125
r_metal_ion_refined0.107
r_chiral_restr0.079
r_bond_refined_d0.012
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_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3029
Nucleic Acid Atoms
Solvent Atoms183
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling
PHASERphasing