☰ Navigation Tabs
Structure of a redesigned cross-reactive antibody to dengue virus with increased in vivo potency
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4UD3 PDB ENTRY 4UD3
Crystallization Crystal Properties Matthews coefficient Solvent content 2.1 41.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.11 α = 90 b = 131.67 β = 90 c = 176.45 γ = 90
Symmetry Space Group P 21 21 21
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 MIRRORS 2014-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA SLS X06DA
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 3.27 105.53 99.9 0.15 4.9 5.4 31554
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 3.27 3.45 99.6 0.49 1.5 5.4
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 PDB ENTRY 4UD3 3.27 48.75 30349 1618 99.76 0.22847 0.22661 0.2253 0.26258 0.2591 RANDOM 51.975
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] -0.02 0.03 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.533 r_dihedral_angle_3_deg 21.929 r_dihedral_angle_4_deg 18.969 r_mcangle_it 4.872 r_dihedral_angle_1_deg 4.72 r_mcbond_it 2.857 r_mcbond_other 2.85 r_scbond_it 2.803 r_angle_other_deg 2.24 r_angle_refined_deg 1.494
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.533 r_dihedral_angle_3_deg 21.929 r_dihedral_angle_4_deg 18.969 r_mcangle_it 4.872 r_dihedral_angle_1_deg 4.72 r_mcbond_it 2.857 r_mcbond_other 2.85 r_scbond_it 2.803 r_angle_other_deg 2.24 r_angle_refined_deg 1.494 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.003 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_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 15068 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing