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Crystal structure of Mtb cyclic dinucleotide phosphodiesterase by sulfur-modified cyclic dinucleotide analogue
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CET This is Apo structure of CdnP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.5 298 0.1 M Sodium Acetate Trihydrate pH 4.5, 2M Sodium Formate (30 % Ethylene Glycol)
Crystal Properties Matthews coefficient Solvent content 2.34 47.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.01 α = 90 b = 149.096 β = 90 c = 167.033 γ = 90
Symmetry Space Group I 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 100 IMAGE PLATE RIGAKU RAXIS 2025-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54179
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.96 51.63 99.86 0.965 4.8 5.1 20959 49.73
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.96 3.14 99.86 1.29 0.39 0.63 0.73 5.1
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 (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 2.96 25.23 19835 1036 99.41 0.22081 0.21817 0.2223 0.27017 0.2752 RANDOM 46.949
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] 0.69 -3.27 2.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.676 r_dihedral_angle_2_deg 9.082 r_long_range_B_other 8.399 r_long_range_B_refined 8.397 r_dihedral_angle_1_deg 6.498 r_mcangle_it 5.986 r_mcangle_other 5.986 r_scangle_other 5.575 r_mcbond_it 3.692 r_mcbond_other 3.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.676 r_dihedral_angle_2_deg 9.082 r_long_range_B_other 8.399 r_long_range_B_refined 8.397 r_dihedral_angle_1_deg 6.498 r_mcangle_it 5.986 r_mcangle_other 5.986 r_scangle_other 5.575 r_mcbond_it 3.692 r_mcbond_other 3.69 r_scbond_it 3.352 r_scbond_other 3.352 r_angle_refined_deg 1.365 r_angle_other_deg 0.478 r_chiral_restr 0.062 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 6909 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement Aimless data scaling MOLREP phasing PDB_EXTRACT data extraction iMOSFLM data reduction