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Protein-aromatic foldamer complex crystal structure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KS3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.7 293 Ammonium sulfate 0.2 M, Sodium acetate 0.1 M pH 5.7, PEG 4000 14%, Sodium azide 3 mM
Crystal Properties Matthews coefficient Solvent content 2.52 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.3 α = 90 b = 80.96 β = 90 c = 45.62 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, CONVEX PREFOCUSSING MIRROR AND A KIRKPATRICK-BAEZ PAIR OF FOCUSSING MIRRORS 2018-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.980112 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.68 45.62 98.6 0.099 0.998 17.96 12.8 8622 72.25
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 2.68 2.84 91.3 0.99 0.859 2.02 12.64
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 3KS3 2.68 45.62 8189 431 98.51 0.21732 0.2148 0.2193 0.26025 0.2629 RANDOM 69.834
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] -4.59 -7.11 11.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.409 r_dihedral_angle_4_deg 19.909 r_dihedral_angle_3_deg 18.245 r_dihedral_angle_1_deg 9.292 r_long_range_B_refined 6.087 r_long_range_B_other 6.086 r_mcangle_other 4.434 r_mcangle_it 4.421 r_scangle_other 3.756 r_mcbond_other 2.653
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.409 r_dihedral_angle_4_deg 19.909 r_dihedral_angle_3_deg 18.245 r_dihedral_angle_1_deg 9.292 r_long_range_B_refined 6.087 r_long_range_B_other 6.086 r_mcangle_other 4.434 r_mcangle_it 4.421 r_scangle_other 3.756 r_mcbond_other 2.653 r_mcbond_it 2.631 r_scbond_it 2.293 r_scbond_other 2.292 r_angle_refined_deg 2.009 r_angle_other_deg 1.551 r_chiral_restr 0.069 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.008 r_gen_planes_other 0.007 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 1778 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms 225
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing