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Hepatitis B capsid Y132A mutant with compound AB-506
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 6.5 289 100 mM ammonium citrate/citric acid pH 6.5, 9%(vol/vol) isopropanol, 10%(wt/vol) PEG 3350, 10% (vol/vol) 2-Methyl-2,4-pentanediol, 0.6:0.3ul at a 2:1 volume ratio at 16C.
Crystal Properties Matthews coefficient Solvent content 2.88 57.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.936 α = 90 b = 87.879 β = 104.12 c = 100.827 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 PIXEL DECTRIS PILATUS 6M 2017-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.978950 CLSI 08ID-1
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 2.5 97.78 99 0.062 0.07200000000000001 0.998 12.78 3.77 44273
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.56 0.263 0.306 0.9840000000000001
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 2.5 97.78 44273 2177 99.1 0.235 0.233 0.2831 0.285 0.3179 RANDOM 77.2
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] -9.81 3.89 -11.6 17.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.49 r_dihedral_angle_4_deg 19.734 r_dihedral_angle_3_deg 16.543 r_mcangle_it 7.628 r_dihedral_angle_1_deg 6.604 r_mcbond_it 4.847 r_mcbond_other 4.846 r_angle_refined_deg 1.497 r_angle_other_deg 1.017 r_chiral_restr 0.075
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.49 r_dihedral_angle_4_deg 19.734 r_dihedral_angle_3_deg 16.543 r_mcangle_it 7.628 r_dihedral_angle_1_deg 6.604 r_mcbond_it 4.847 r_mcbond_other 4.846 r_angle_refined_deg 1.497 r_angle_other_deg 1.017 r_chiral_restr 0.075 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6618 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 224
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data reduction PHASER phasing