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Crystal Structure of Mycobacterium Tuberculosis Proteasome in complex with a peptidyl boronate inhibitor MLN-273
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Q5Q PDB ENTRY 1Q5Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.7 293 8% PEG 6000, 50 mM sodium citrate, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.54 51.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 173.957 α = 90 b = 116.172 β = 112.71 c = 200.203 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 CCD ADSC QUANTUM 4 2005-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.0 NSLS X25
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.99 50 0.944 0.058 18.6 398981 139848 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.99 3.11 0.844 0.25 2.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1Q5Q 2.99 50 2 139848 132804 7037 94.12 0.228 0.22814 0.22636 0.2274 0.26163 0.2294 RANDOM 85.398
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] 3.28 3.52 1.05 -1.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.054 r_dihedral_angle_3_deg 21.075 r_dihedral_angle_4_deg 18.922 r_dihedral_angle_1_deg 4.857 r_scangle_it 1.69 r_angle_refined_deg 1.298 r_mcangle_it 1.006 r_scbond_it 0.949 r_mcbond_it 0.571 r_symmetry_vdw_refined 0.412
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.054 r_dihedral_angle_3_deg 21.075 r_dihedral_angle_4_deg 18.922 r_dihedral_angle_1_deg 4.857 r_scangle_it 1.69 r_angle_refined_deg 1.298 r_mcangle_it 1.006 r_scbond_it 0.949 r_mcbond_it 0.571 r_symmetry_vdw_refined 0.412 r_nbtor_refined 0.308 r_nbd_refined 0.241 r_symmetry_hbond_refined 0.231 r_xyhbond_nbd_refined 0.166 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 46620 Nucleic Acid Atoms Solvent Atoms 321 Heterogen Atoms 448
Software Software Software Name Purpose REFMAC refinement CBASS data collection SCALEPACK data scaling CNS phasing