☰ Navigation Tabs
Nanobody H3 AND C1 bound to RBD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ZBP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1.0 M Lithium chloride, 0.1 M Citrate pH 4, 20 % Peg 6000
Crystal Properties Matthews coefficient Solvent content 2.94 58.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.683 α = 90 b = 105.683 β = 90 c = 112.539 γ = 90
Symmetry Space Group P 43 21 2
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 2020-09-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim 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 1.9 62.254 100 0.025 0.99 14.4 25.4 50645
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 1.9 1.95 100 0.94 0.7 22.1
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6ZBP 1.901 62.254 50645 2656 99.923 0.182 0.1802 0.204 0.1885 44.25
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] 0.759 0.759 -1.518
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.989 r_dihedral_angle_4_deg 14.764 r_dihedral_angle_3_deg 13.46 r_dihedral_angle_1_deg 7.375 r_lrange_other 7.254 r_lrange_it 7.253 r_scangle_it 4.978 r_scangle_other 4.977 r_scbond_it 3.37 r_scbond_other 3.194
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.989 r_dihedral_angle_4_deg 14.764 r_dihedral_angle_3_deg 13.46 r_dihedral_angle_1_deg 7.375 r_lrange_other 7.254 r_lrange_it 7.253 r_scangle_it 4.978 r_scangle_other 4.977 r_scbond_it 3.37 r_scbond_other 3.194 r_mcangle_other 2.938 r_mcangle_it 2.937 r_mcbond_it 2.04 r_mcbond_other 2.036 r_angle_refined_deg 1.528 r_angle_other_deg 1.342 r_symmetry_nbd_refined 0.235 r_nbd_other 0.22 r_nbd_refined 0.192 r_symmetry_nbd_other 0.175 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.146 r_symmetry_xyhbond_nbd_refined 0.135 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.068 r_symmetry_xyhbond_nbd_other 0.04 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3509 Nucleic Acid Atoms Solvent Atoms 235 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing