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Crystal structure of HBV capsid with compound 18
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5E0I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 13-18% (v/v) MPD, 280-310 mM trisodium citrate, and 100 mM Hepes pH 7.5. Protein:reservoir ratio of 2:1
Crystal Properties Matthews coefficient Solvent content 3.02 59.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.152 α = 90 b = 88.152 β = 90 c = 290.557 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 PIXEL DECTRIS PILATUS3 S 6M 2019-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.54 48.473 99.8 0.124 0.132 0.044 0.999 8.2 8.6 14719
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.54 2.66 99.4 0.921 0.982 0.336 0.924 1.9 8.3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.543 48.473 14719 779 99.79 0.262 0.2605 0.2695 0.2966 0.2986 88.676
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] -8.776 -4.388 -8.776 28.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.027 r_lrange_other 15.051 r_lrange_it 15.04 r_dihedral_angle_6_deg 14.665 r_mcangle_it 10.568 r_mcangle_other 10.568 r_scangle_it 10.196 r_scangle_other 10.193 r_dihedral_angle_1_deg 7.066 r_mcbond_it 6.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.027 r_lrange_other 15.051 r_lrange_it 15.04 r_dihedral_angle_6_deg 14.665 r_mcangle_it 10.568 r_mcangle_other 10.568 r_scangle_it 10.196 r_scangle_other 10.193 r_dihedral_angle_1_deg 7.066 r_mcbond_it 6.59 r_mcbond_other 6.584 r_scbond_it 6.123 r_scbond_other 6.121 r_dihedral_angle_2_deg 5.008 r_angle_refined_deg 1.483 r_angle_other_deg 0.799 r_nbd_refined 0.251 r_xyhbond_nbd_refined 0.225 r_symmetry_nbd_other 0.221 r_nbd_other 0.21 r_nbtor_refined 0.194 r_symmetry_xyhbond_nbd_refined 0.168 r_symmetry_xyhbond_nbd_other 0.154 r_symmetry_nbd_refined 0.134 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.059 r_gen_planes_other 0.006 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2118 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing