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Crystal structure of the HBV capsid Y132A mutant (VCID 8772) in complex with NVR10-001E2 at 1.95A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BMG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 290 0.1M AMMONIUM CITRATE/CITRIC ACID
PH 6.5, 9% ISOPROPANOL, 10% PEG 3350, 10% MPD, VAPOR
DIFFUSION, TEMPERATURE 293K
Crystal Properties Matthews coefficient Solvent content 3.36 61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 152.6 α = 90 b = 88.17 β = 103.47 c = 102.25 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 RAYONIX MX-225 2013-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.95 50 99.9 0.098 11.35 4.74 96089 95947 -3 26.35
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 100 0.506 3.1 4.77
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 4BMG 1.95 50 95947 4810 99.89 0.221 0.219 0.2316 0.252 0.2618 RANDOM 29.73
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] -1.56 0.52 -1.79 2.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.642 r_dihedral_angle_4_deg 19.613 r_dihedral_angle_3_deg 13.738 r_dihedral_angle_1_deg 6.115 r_angle_refined_deg 1.701 r_mcangle_it 1.698 r_mcbond_it 1.06 r_mcbond_other 1.058 r_angle_other_deg 0.928 r_chiral_restr 0.096
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.642 r_dihedral_angle_4_deg 19.613 r_dihedral_angle_3_deg 13.738 r_dihedral_angle_1_deg 6.115 r_angle_refined_deg 1.701 r_mcangle_it 1.698 r_mcbond_it 1.06 r_mcbond_other 1.058 r_angle_other_deg 0.928 r_chiral_restr 0.096 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 6864 Nucleic Acid Atoms Solvent Atoms 440 Heterogen Atoms 180
Software Software Software Name Purpose XDS data reduction XSCALE data scaling Coot model building PHASER phasing REFMAC refinement