8IBO

Crystal structure of Wild-Type Mycobacterium tuberculosis ClpC1 N-terminal domain in complex with Lassomycin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3WDB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52911.4 M sodium acetate, 0.1 M sodium cacodylate (pH 6.5)
Crystal Properties
Matthews coefficientSolvent content
2.5752.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.431α = 90
b = 58.468β = 90
c = 64.763γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray103CCDMARMOSAIC 225 mm CCD2019-09-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONRRCAT INDUS-2 BEAMLINE PX-BL210.9794RRCAT INDUS-2PX-BL21

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
11.8336.861000.03830.47.616474
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)
11.831.870.4974

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.8336.861560582199.90.1850.1830.236RANDOM35.99
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]
2.36-1.18-1.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.734
r_dihedral_angle_4_deg17.836
r_dihedral_angle_3_deg13.781
r_long_range_B_other9.157
r_long_range_B_refined9.152
r_scangle_other7.247
r_dihedral_angle_1_deg6.441
r_scbond_it5.323
r_scbond_other5.319
r_mcangle_it4.867
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.734
r_dihedral_angle_4_deg17.836
r_dihedral_angle_3_deg13.781
r_long_range_B_other9.157
r_long_range_B_refined9.152
r_scangle_other7.247
r_dihedral_angle_1_deg6.441
r_scbond_it5.323
r_scbond_other5.319
r_mcangle_it4.867
r_mcangle_other4.864
r_mcbond_it3.877
r_mcbond_other3.832
r_angle_refined_deg1.546
r_angle_other_deg1.226
r_chiral_restr0.097
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1236
Nucleic Acid Atoms
Solvent Atoms57
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing