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Crystal Structure of M. tuberculosis YefM antitoxin
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.2 298 10% PEG 1000, 0.1M sodium phosphate citrate, 0.5M lithium sulphate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.71719 28.371336
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.003 α = 90 b = 64.573 β = 90 c = 83.518 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 77 CCD MARRESEARCH 2005-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.2 ELETTRA 5.2R
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 2.5 50 98.2 0.059 22.3 4.9 12668 12447 44.4
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 2.5 2.59 96.5 0.188 8.5 7.2 1222
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 2.5 19.95 12447 11809 605 98.41 0.20767 0.20528 0.2031 0.25452 0.2504 RANDOM 42.039
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] -0.15 0.05 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.185 r_dihedral_angle_3_deg 20.985 r_dihedral_angle_4_deg 19.6 r_dihedral_angle_1_deg 5.968 r_scangle_it 3.677 r_scbond_it 2.238 r_angle_refined_deg 1.604 r_mcangle_it 1.292 r_mcbond_it 0.786 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.185 r_dihedral_angle_3_deg 20.985 r_dihedral_angle_4_deg 19.6 r_dihedral_angle_1_deg 5.968 r_scangle_it 3.677 r_scbond_it 2.238 r_angle_refined_deg 1.604 r_mcangle_it 1.292 r_mcbond_it 0.786 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.27 r_nbd_refined 0.223 r_symmetry_hbond_refined 0.173 r_xyhbond_nbd_refined 0.166 r_chiral_restr 0.119 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2515 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection DENZO data reduction SCALEPACK data scaling AMoRE phasing