2FHH

Crystal Structure of Mycobacterium Tuberculosis Proteasome in complex with a peptidyl boronate inhibitor MLN-273


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Q5QPDB ENTRY 1Q5Q

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.72938% PEG 6000, 50 mM sodium citrate, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5451.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 173.957α = 90
b = 116.172β = 112.71
c = 200.203γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDADSC QUANTUM 42005-02-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X251.0NSLSX25

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
12.99500.9440.05818.639898113984822
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)
12.993.110.8440.252.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1Q5Q2.99502139848132804703794.120.2280.228140.226360.26163RANDOM85.398
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]
3.283.521.05-1.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.054
r_dihedral_angle_3_deg21.075
r_dihedral_angle_4_deg18.922
r_dihedral_angle_1_deg4.857
r_scangle_it1.69
r_angle_refined_deg1.298
r_mcangle_it1.006
r_scbond_it0.949
r_mcbond_it0.571
r_symmetry_vdw_refined0.412
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.054
r_dihedral_angle_3_deg21.075
r_dihedral_angle_4_deg18.922
r_dihedral_angle_1_deg4.857
r_scangle_it1.69
r_angle_refined_deg1.298
r_mcangle_it1.006
r_scbond_it0.949
r_mcbond_it0.571
r_symmetry_vdw_refined0.412
r_nbtor_refined0.308
r_nbd_refined0.241
r_symmetry_hbond_refined0.231
r_xyhbond_nbd_refined0.166
r_chiral_restr0.086
r_bond_refined_d0.01
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms46620
Nucleic Acid Atoms
Solvent Atoms321
Heterogen Atoms448

Software

Software
Software NamePurpose
REFMACrefinement
CBASSdata collection
SCALEPACKdata scaling
CNSphasing