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Crystal structure of Rv2186c in Mycobacterium tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.1 289 0.1M Tris-HCl, pH7.1, 0.3M MgCl2, 10% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.2 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.477 α = 90 b = 28.254 β = 100.771 c = 86.779 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 80 CCD MARMOSAIC 225 mm CCD 2021-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97915 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) 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 1.56 50 95.9 0.074 0.029 0.98 27.8 6.6 36125
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.56 1.59 0.329 0.138 0.949
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.563 27.291 36125 1799 98.519 0.16 0.1578 0.1579 0.2038 0.2039 Random selection 22.84
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] -0.966 -0.564 1.182 -0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.951 r_dihedral_angle_3_deg 13.838 r_dihedral_angle_2_deg 12.723 r_dihedral_angle_1_deg 6.617 r_rigid_bond_restr 4.542 r_lrange_it 3.993 r_lrange_other 3.915 r_scangle_it 3.182 r_scangle_other 3.181 r_mcangle_other 2.682
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.951 r_dihedral_angle_3_deg 13.838 r_dihedral_angle_2_deg 12.723 r_dihedral_angle_1_deg 6.617 r_rigid_bond_restr 4.542 r_lrange_it 3.993 r_lrange_other 3.915 r_scangle_it 3.182 r_scangle_other 3.181 r_mcangle_other 2.682 r_mcangle_it 2.675 r_scbond_it 2.352 r_scbond_other 2.351 r_mcbond_it 2.044 r_mcbond_other 2.039 r_angle_refined_deg 1.633 r_angle_other_deg 0.585 r_symmetry_nbd_refined 0.305 r_nbd_other 0.253 r_nbd_refined 0.223 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.179 r_symmetry_xyhbond_nbd_refined 0.178 r_xyhbond_nbd_refined 0.148 r_ncsr_local_group_1 0.129 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1950 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing