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HBV CAPSID Y132A WITH COMPOUND 10b AT 2.5A RESOLUTION
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 7 289 10% PEG 3350, 10 to 14% (+/-)-2-methyl-2,4-pentanediol (MPD), 8 to 10% isopropanol, and 100 mM ammonium citrate/citric acid
Crystal Properties Matthews coefficient Solvent content 3.14 60.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 152.239 α = 90 b = 88.306 β = 103.89 c = 103.712 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 93 PIXEL DECTRIS PILATUS3 6M 2018-08-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.976251 ESRF ID30B
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 2.5 50 99.4 0.99 5.4 3.33 46072
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 2.5 2.65 98.9 0.742 1.06
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 5E0I 2.5 47.26 43745 2307 99.4 0.271 0.2696 0.3101 0.2975 0.3402 RANDOM 67.483
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] -7.38 2.21 -7.75 12.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.633 r_dihedral_angle_4_deg 24.598 r_dihedral_angle_3_deg 20.296 r_dihedral_angle_1_deg 7.227 r_angle_refined_deg 1.661 r_angle_other_deg 1.152 r_chiral_restr 0.052 r_gen_planes_refined 0.012 r_gen_planes_other 0.007 r_bond_refined_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.633 r_dihedral_angle_4_deg 24.598 r_dihedral_angle_3_deg 20.296 r_dihedral_angle_1_deg 7.227 r_angle_refined_deg 1.661 r_angle_other_deg 1.152 r_chiral_restr 0.052 r_gen_planes_refined 0.012 r_gen_planes_other 0.007 r_bond_refined_d 0.006 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6280 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 186
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing