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X-ray structure of HCA(II)/aromatic foldamer complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Q9T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.8 293 0.2M Lithium sulfate, 0.1M TRIS pH 8.8, 18% PEG 4000, 3mM sodium azide
Crystal Properties Matthews coefficient Solvent content 2.57 52.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.25 α = 90 b = 81.29 β = 90 c = 46.12 γ = 90
Symmetry Space Group P 21 21 2
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 9M Cryogenically cooled channel cut crystal monochromator, a convex prefocussing mirror and a Kirkpatrick-Baez pair of focussing mirrors 2019-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.979995 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.11 50 99.5 0.107 0.117 0.998 10.79 6.5 17876
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.11 2.24 97.1 1.459 0.557 1.22 6.57
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 2.11 46.12 16979 894 99.47 0.20302 0.20033 0.2064 0.25244 0.2575 RANDOM 50.084
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] -1.56 -2.29 3.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.361 r_dihedral_angle_2_deg 8.278 r_dihedral_angle_1_deg 8.198 r_long_range_B_refined 7.297 r_long_range_B_other 7.296 r_scangle_other 5.315 r_mcangle_other 4.625 r_mcangle_it 4.618 r_scbond_it 3.377 r_scbond_other 3.376
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.361 r_dihedral_angle_2_deg 8.278 r_dihedral_angle_1_deg 8.198 r_long_range_B_refined 7.297 r_long_range_B_other 7.296 r_scangle_other 5.315 r_mcangle_other 4.625 r_mcangle_it 4.618 r_scbond_it 3.377 r_scbond_other 3.376 r_mcbond_it 3.187 r_mcbond_other 3.181 r_angle_refined_deg 1.035 r_angle_other_deg 0.421 r_chiral_restr 0.051 r_gen_planes_refined 0.009 r_bond_refined_d 0.007 r_gen_planes_other 0.002 r_bond_other_d 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 2042 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms 254
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction