8IVP

Crystal structure of MV in complex with LLP and FRU from Mycobacterium vanbaalenii


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2980.2 M lithium sulfate,0.1M Tris, pH 8.5,1.26M ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.6252.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.707α = 90
b = 112.243β = 112.31
c = 92.098γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2022-10-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL18U11.0SSRFBL18U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.925093.20.1150.1260.050.99111.16.3106452
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.921.9990.60.5450.5950.2320.7676.2

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 REPLACEMENTTHROUGHOUT1.9345.14101032534492.70.1530.1510.188RANDOM16.54
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]
-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.78
r_dihedral_angle_4_deg20.387
r_dihedral_angle_3_deg13.782
r_dihedral_angle_1_deg6.97
r_long_range_B_refined5.669
r_long_range_B_other5.325
r_scangle_other3.563
r_scbond_it2.335
r_scbond_other2.334
r_mcangle_it1.969
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.78
r_dihedral_angle_4_deg20.387
r_dihedral_angle_3_deg13.782
r_dihedral_angle_1_deg6.97
r_long_range_B_refined5.669
r_long_range_B_other5.325
r_scangle_other3.563
r_scbond_it2.335
r_scbond_other2.334
r_mcangle_it1.969
r_mcangle_other1.969
r_angle_refined_deg1.678
r_angle_other_deg1.395
r_mcbond_it1.366
r_mcbond_other1.365
r_chiral_restr0.076
r_bond_refined_d0.012
r_gen_planes_refined0.01
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 Atoms9914
Nucleic Acid Atoms
Solvent Atoms1534
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
Aimlessdata scaling
PHASERphasing
HKL-2000data reduction