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Structure of the Mycobacterium tuberculosis protein, Rv2275, demonstrates that cyclodipeptide synthetases are related to type I tRNA-Synthetases.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.75 12-15% (W/V) PEG 8000, 1M LICL, 100 MM TRIS/BICINE, PH 8.75
Crystal Properties Matthews coefficient Solvent content 2.99 58.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.09 α = 90 b = 75.06 β = 90 c = 140.36 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 193 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X9A NSLS X9A
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 39 98.9 0.07 13.5 5.3 49827 27.1
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 2.12 95.9 0.41 3.6 4.6
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 SAD THROUGHOUT NONE 2.02 70.18 47238 2525 98.78 0.18142 0.17983 0.1857 0.21047 0.2168 RANDOM 32.091
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] 1.38 -1.52 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.277 r_dihedral_angle_4_deg 19.541 r_dihedral_angle_3_deg 14.815 r_scangle_it 6.643 r_dihedral_angle_1_deg 5.938 r_scbond_it 4.244 r_mcangle_it 2.492 r_angle_refined_deg 2.047 r_mcbond_it 1.403 r_chiral_restr 0.163
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.277 r_dihedral_angle_4_deg 19.541 r_dihedral_angle_3_deg 14.815 r_scangle_it 6.643 r_dihedral_angle_1_deg 5.938 r_scbond_it 4.244 r_mcangle_it 2.492 r_angle_refined_deg 2.047 r_mcbond_it 1.403 r_chiral_restr 0.163 r_bond_refined_d 0.027 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3540 Nucleic Acid Atoms Solvent Atoms 264 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHENIX phasing