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NSP14 IN COMPLEX WITH LIGAND TDI-014925-CL-2 (compound 58)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7R2V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 277 isopropanol and imidazole, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.4 48.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.458 α = 90 b = 100.962 β = 108.33 c = 90.426 γ = 90
Symmetry Space Group P 1 21 1
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 EIGER2 S 16M 2023-03-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9999 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (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 2.377 64.12 99.5 0.096 0.096 0.093 0.05 0.997 9.3 4.4 46172
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.377 2.418 98.8 2.333 2.333 0.988 0.376 1.3 4.3
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 2.38 64.12 44432 1125 98.17 0.19435 0.19314 0.1947 0.24517 0.2428 RANDOM 63.702
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] -2.31 -0.46 3.78 -0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.865 r_dihedral_angle_3_deg 15.294 r_dihedral_angle_4_deg 12.897 r_long_range_B_other 8.932 r_long_range_B_refined 8.927 r_dihedral_angle_1_deg 7.686 r_scangle_other 6.58 r_mcangle_it 6.353 r_mcangle_other 6.353 r_scbond_it 4.223
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.865 r_dihedral_angle_3_deg 15.294 r_dihedral_angle_4_deg 12.897 r_long_range_B_other 8.932 r_long_range_B_refined 8.927 r_dihedral_angle_1_deg 7.686 r_scangle_other 6.58 r_mcangle_it 6.353 r_mcangle_other 6.353 r_scbond_it 4.223 r_scbond_other 4.223 r_mcbond_it 4.209 r_mcbond_other 4.208 r_angle_refined_deg 1.502 r_angle_other_deg 1.161 r_chiral_restr 0.061 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 7043 Nucleic Acid Atoms Solvent Atoms 207 Heterogen Atoms 141
Software Software Software Name Purpose autoPROC data reduction XDS data reduction XDS data reduction autoPROC data scaling Aimless data scaling REFMAC refinement XDS data scaling PDB_EXTRACT data extraction PHASES phasing