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HBV capsid with compound 3i
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 289 10% PEG 3350, 10 to 14% (+/-)-2-methyl-2,4-pentanediol (MPD), 8 to 10%
isopropanol, and 100 mM ammonium citrate/citric acid pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.12 60.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.944 α = 90 b = 87.919 β = 102.748 c = 108.503 γ = 90
Symmetry Space Group C 1 2 1
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 MAR CCD 130 mm 2018-08-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID13 0.97625 ESRF ID13
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 2.63 50 98.7 0.937 6.1 3.3 41271
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 2.63 2.72 0.609
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 2.63 48.409 41046 2055 98.611 0.226 0.2239 0.2311 0.258 0.2602 72.001
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] -0.935 -0.235 -0.743 1.618
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.504 r_dihedral_angle_6_deg 14.286 r_lrange_it 11.805 r_lrange_other 11.804 r_mcangle_it 9.056 r_mcangle_other 9.055 r_scangle_it 8.388 r_scangle_other 8.387 r_dihedral_angle_1_deg 7.312 r_dihedral_angle_2_deg 6.683
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.504 r_dihedral_angle_6_deg 14.286 r_lrange_it 11.805 r_lrange_other 11.804 r_mcangle_it 9.056 r_mcangle_other 9.055 r_scangle_it 8.388 r_scangle_other 8.387 r_dihedral_angle_1_deg 7.312 r_dihedral_angle_2_deg 6.683 r_mcbond_it 5.742 r_mcbond_other 5.733 r_scbond_it 5.29 r_scbond_other 5.289 r_angle_refined_deg 1.752 r_angle_other_deg 0.625 r_nbd_refined 0.247 r_symmetry_nbd_other 0.205 r_nbtor_refined 0.198 r_xyhbond_nbd_refined 0.186 r_symmetry_xyhbond_nbd_other 0.169 r_nbd_other 0.169 r_symmetry_nbd_refined 0.1 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.075 r_symmetry_xyhbond_nbd_refined 0.073 r_gen_planes_refined 0.009 r_gen_planes_other 0.009 r_bond_refined_d 0.008 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6235 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 174
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing