☰ Navigation Tabs
Nanobody H11-H4 Q98R H100E 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 0.2M Ammonium nitrate, 20 % Peg 3350
Crystal Properties Matthews coefficient Solvent content 2.89 57.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.243 α = 90 b = 78.243 β = 90 c = 126.812 γ = 120
Symmetry Space Group P 31 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 EIGER2 XE 16M 2021-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.59 67.761 100 0.046 0.999 24.9 18.8 61104
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.59 1.62 100 4.156 0.361 0.4 20.2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6ZBP 1.59 67.761 61035 3095 99.972 0.163 0.161 0.1739 0.2023 0.2137 38.799
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] -0.473 -0.237 -0.473 1.535
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.597 r_dihedral_angle_4_deg 15.032 r_dihedral_angle_3_deg 11.691 r_dihedral_angle_1_deg 6.994 r_lrange_other 4.131 r_lrange_it 4.128 r_scangle_it 3.287 r_scangle_other 3.237 r_mcangle_other 3.055 r_mcangle_it 3.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.597 r_dihedral_angle_4_deg 15.032 r_dihedral_angle_3_deg 11.691 r_dihedral_angle_1_deg 6.994 r_lrange_other 4.131 r_lrange_it 4.128 r_scangle_it 3.287 r_scangle_other 3.237 r_mcangle_other 3.055 r_mcangle_it 3.05 r_scbond_it 2.621 r_scbond_other 2.527 r_mcbond_it 2.307 r_mcbond_other 2.293 r_rigid_bond_restr 1.36 r_angle_refined_deg 1.306 r_angle_other_deg 1.267 r_symmetry_nbd_refined 0.266 r_nbd_other 0.215 r_nbd_refined 0.186 r_symmetry_nbd_other 0.178 r_nbtor_refined 0.171 r_symmetry_xyhbond_nbd_refined 0.147 r_xyhbond_nbd_refined 0.123 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.061 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2520 Nucleic Acid Atoms Solvent Atoms 206 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing