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Coevolved affibody-Z domain pair LL2.c17
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DJT 5djt
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.2 295 2.3 M Amm2HPO4, 100 mM Tris pH 8.2
cryoprotected in 30% glycerol
Crystal Properties Matthews coefficient Solvent content 1.97 37.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.091 α = 90 b = 35.532 β = 115.42 c = 49.433 γ = 90
Symmetry Space Group C 1 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 PILATUS 6M 2022-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.77488 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.134 31.65 60.77 0.09152 0.09654 0.03031 0.999 15.86 9.8 27318 12.19
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.134 1.175 3.1 4.141 4.383 1.415 0.321 1.21 9.4
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5djt 1.134 31.65 1.34 27307 1528 60.77 0.1738 0.1723 0.1728 0.1995 0.2001 random selection 18.88
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 12.6379 f_angle_d 0.8283 f_chiral_restr 0.0563 f_plane_restr 0.0094 f_bond_d 0.0068
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 845 Nucleic Acid Atoms Solvent Atoms 148 Heterogen Atoms
Software Software Software Name Purpose Blu-Ice data collection PHENIX refinement DIALS data reduction STARANISO data scaling PHASER phasing BUSTER refinement XDS data reduction Aimless data scaling