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TC:CD320 in complex with nanobody TC-Nb4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZRP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 300 100 mM Bis-Tris pH 5.5, 25% w/v PEG 3350, supplemented with 10% (0.2% w/v Betaine anhydrous, 0.2% w/v L-Glutamic acid, 0.2% w/v L-Proline, 0.2% w/v Taurine, 0.2% w/v Trimethylamine N-oxide dihydrate, 0.02 M HEPES sodium pH 6.8
Crystal Properties Matthews coefficient Solvent content 2.53 51.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.339 α = 90 b = 116.418 β = 90 c = 125.498 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 EIGER X 16M 2016-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.979502 SLS X06SA
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 2.69 48.92 97.98 0.993 7.97 2 84243 56.39
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 2.69 2.79 0.459
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4ZRP 2.69 48.92 1.2 80419 4022 97.39 0.2299 0.227 0.2268 0.2854 0.2836 63.61
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 24.1663 f_angle_d 2.025 f_chiral_restr 0.1193 f_plane_restr 0.0123 f_bond_d 0.0106
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9092 Nucleic Acid Atoms Solvent Atoms 47 Heterogen Atoms 210
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing