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Crystal structure of dimethylated RSL - cucurbit[7]uril complex, C2221 Form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BT9 2bt9 chain A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 20% PEG 3350
200 mM Sodium Malonate pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.76 55.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.343 α = 90 b = 87.176 β = 90 c = 146.595 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 CCD ADSC QUANTUM 315 2017-08-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9791 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.28 43.6 95 0.05 0.022 0.99 18.8 4.5 78616
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.28 1.3 92.4 0.501 0.38 0.706 1.9 4
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 2bt9 chain A 1.28 43.6 74734 3865 94.49 0.1249 0.1236 0.1238 0.1508 0.1513 RANDOM 18.503
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] -0.36 1.05 -0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.493 r_sphericity_free 28.573 r_sphericity_bonded 9.865 r_dihedral_angle_3_deg 9.62 r_dihedral_angle_1_deg 6.651 r_dihedral_angle_4_deg 3.735 r_rigid_bond_restr 1.455 r_angle_refined_deg 1.328 r_angle_other_deg 1.011 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.493 r_sphericity_free 28.573 r_sphericity_bonded 9.865 r_dihedral_angle_3_deg 9.62 r_dihedral_angle_1_deg 6.651 r_dihedral_angle_4_deg 3.735 r_rigid_bond_restr 1.455 r_angle_refined_deg 1.328 r_angle_other_deg 1.011 r_chiral_restr 0.085 r_gen_planes_refined 0.015 r_bond_refined_d 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2070 Nucleic Acid Atoms Solvent Atoms 385 Heterogen Atoms 301
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction