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Crystal structure of compound 8t bound to PaLpxC
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5UPG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 100 mM Tris pH 7.4, 32% PEG Smear Medium, 2% glycerol, 2 mM TCEP
Crystal Properties Matthews coefficient Solvent content 2.98 58.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.745 α = 90 b = 108.745 β = 90 c = 58.261 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD APEX II CCD 2020-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5406
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 1.9 36.62 100 0.999 12.2 1.9 31043
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.902 1.951 98.7 1 1.8
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 1.902 35.621 31026 1606 99.942 0.2 0.1979 0.2006 0.2299 0.2376 31.624
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] 0.532 0.266 0.532 -1.725
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.939 r_dihedral_angle_3_deg 13.609 r_dihedral_angle_2_deg 9.806 r_lrange_it 8.989 r_lrange_other 8.985 r_dihedral_angle_1_deg 7.035 r_scangle_other 6.551 r_scangle_it 6.546 r_mcangle_it 4.646 r_mcangle_other 4.644
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.939 r_dihedral_angle_3_deg 13.609 r_dihedral_angle_2_deg 9.806 r_lrange_it 8.989 r_lrange_other 8.985 r_dihedral_angle_1_deg 7.035 r_scangle_other 6.551 r_scangle_it 6.546 r_mcangle_it 4.646 r_mcangle_other 4.644 r_scbond_it 4.252 r_scbond_other 4.246 r_mcbond_it 3.049 r_mcbond_other 3.048 r_angle_refined_deg 1.763 r_angle_other_deg 0.598 r_symmetry_xyhbond_nbd_refined 0.215 r_nbd_refined 0.204 r_symmetry_nbd_refined 0.198 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.168 r_nbd_other 0.141 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2348 Nucleic Acid Atoms Solvent Atoms 157 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement