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Crystal Structure of Mycobacterium Tuberculosis Proteasome-assembly chaperone homologue Rv2125
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MNF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1 M sodium chloride, 0.1 M HEPES pH 7.5, 1.6 M ammonium sulfate, 1% w/v ANAPOE-20, and 2% w/v benzamidine hydrochloride
Crystal Properties Matthews coefficient Solvent content 2.89 57.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.25 α = 90 b = 79.76 β = 103.57 c = 89.03 γ = 90
Symmetry Space Group C 1 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 315 2014-07-01 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 315 2014-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.1 NSLS X25 2 SYNCHROTRON NSLS BEAMLINE X29A 1.1 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3 30.65 98.9 5.7 3.6 18826
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 3mnf 3 30.65 17881 951 98.83 0.23905 0.23643 0.2371 0.28914 0.2908 RANDOM 40.831
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] -0.13 0.37 -0.41 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.463 r_dihedral_angle_4_deg 20.146 r_dihedral_angle_3_deg 18.889 r_long_range_B_refined 8.941 r_long_range_B_other 8.934 r_dihedral_angle_1_deg 7.304 r_scangle_other 4.98 r_mcangle_it 3.855 r_mcangle_other 3.855 r_angle_other_deg 3.694
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.463 r_dihedral_angle_4_deg 20.146 r_dihedral_angle_3_deg 18.889 r_long_range_B_refined 8.941 r_long_range_B_other 8.934 r_dihedral_angle_1_deg 7.304 r_scangle_other 4.98 r_mcangle_it 3.855 r_mcangle_other 3.855 r_angle_other_deg 3.694 r_scbond_it 3.19 r_scbond_other 3.189 r_mcbond_it 2.221 r_mcbond_other 2.217 r_angle_refined_deg 1.381 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_gen_planes_other 0.005 r_bond_other_d 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 5430 Nucleic Acid Atoms Solvent Atoms 86 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing