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Nanobody2 in complex with human BCMA ECD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5BOP experimental model PDB 1XU2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 1.8 M Sodium acetate trihydrate,
0.1 M Bis-Tris Propane pH7.0
Crystal Properties Matthews coefficient Solvent content 3.24 62.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.062 α = 90 b = 80.062 β = 90 c = 78.955 γ = 90
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 2020-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.978 SSRF BL17U1
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 2.7 50 99.8 0.973 6.25 4.6 13801
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 2.7 2.86 0.623
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.7 40.03 13778 684 99.8 0.24 0.2388 0.287 0.2809 29.82
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.324 f_angle_d 0.6563 f_chiral_restr 0.0409 f_bond_d 0.0032 f_plane_restr 0.0032
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2446 Nucleic Acid Atoms Solvent Atoms 77 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing