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Crystal Structure of CntL in complex with a dual-site inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7C7M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 0.23 M Calcium acetate, 0.1 M Sodium cacodylate 6.4, 35% PEG 300, 1.5% iBu
Crystal Properties Matthews coefficient Solvent content 1.97 37.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.395 α = 90 b = 135.511 β = 90 c = 131.814 γ = 90
Symmetry Space Group C 2 2 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 PIXEL DECTRIS EIGER X 16M 2021-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.97914 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.09 67.76 97.1 0.072 0.998 9.5 5.1 29426
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.09 2.2 100 0.853 0.668 5.4
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.091 67.756 29384 1475 96.974 0.203 0.2014 0.2056 0.2393 0.239 41.628
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] 3.585 -2.244 -1.342
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.447 r_dihedral_angle_6_deg 15.2 r_dihedral_angle_2_deg 8.154 r_lrange_it 6.859 r_lrange_other 6.846 r_dihedral_angle_1_deg 5.623 r_scangle_it 4.382 r_scangle_other 4.381 r_mcangle_other 2.908 r_mcangle_it 2.906
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.447 r_dihedral_angle_6_deg 15.2 r_dihedral_angle_2_deg 8.154 r_lrange_it 6.859 r_lrange_other 6.846 r_dihedral_angle_1_deg 5.623 r_scangle_it 4.382 r_scangle_other 4.381 r_mcangle_other 2.908 r_mcangle_it 2.906 r_scbond_it 2.775 r_scbond_other 2.774 r_mcbond_it 1.85 r_mcbond_other 1.85 r_angle_refined_deg 1.175 r_angle_other_deg 0.418 r_symmetry_nbd_refined 0.232 r_nbd_other 0.209 r_nbd_refined 0.208 r_symmetry_nbd_other 0.202 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.147 r_symmetry_xyhbond_nbd_refined 0.131 r_symmetry_metal_ion_refined 0.09 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.058 r_symmetry_xyhbond_nbd_other 0.029 r_metal_ion_refined 0.013 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3701 Nucleic Acid Atoms Solvent Atoms 109 Heterogen Atoms 97
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling MOLREP phasing