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complete structure of the Mycobacterium tuberculosis proteasomal ATPase Mpa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3M9B 3M9B, 3WHK experimental model PDB 3WHK 3M9B, 3WHK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.2 288 100mM Tris-HCl, 20%PEG400, 200mM MgCl2, 5mM ATPrS
Crystal Properties Matthews coefficient Solvent content 3.22 61.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.931 α = 90 b = 111.931 β = 90 c = 196.072 γ = 120
Symmetry Space Group P 3 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2013-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9791 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.9 43.45 100 0.112 0.984 7 10.6 32237 56.52
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3.06 100 0.703 0.506 10.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 3M9B, 3WHK 2.9 43.45 30678 1543 99.89 0.22974 0.22786 0.2296 0.26883 0.266 RANDOM 61.887
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] -1.49 -0.75 -1.49 4.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.032 r_dihedral_angle_3_deg 16.497 r_dihedral_angle_4_deg 14.204 r_long_range_B_refined 6.551 r_long_range_B_other 6.551 r_dihedral_angle_1_deg 6.044 r_mcangle_it 3.992 r_mcangle_other 3.992 r_scangle_other 3.876 r_mcbond_it 2.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.032 r_dihedral_angle_3_deg 16.497 r_dihedral_angle_4_deg 14.204 r_long_range_B_refined 6.551 r_long_range_B_other 6.551 r_dihedral_angle_1_deg 6.044 r_mcangle_it 3.992 r_mcangle_other 3.992 r_scangle_other 3.876 r_mcbond_it 2.305 r_mcbond_other 2.303 r_scbond_it 2.192 r_scbond_other 2.189 r_angle_refined_deg 1.309 r_angle_other_deg 0.926 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 7102 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing