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Coevolved affibody-Z domain pair LL2.c22
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 2.5 M AmmSO4, 100 mM Tris pH 8.2
Cryoprotected with 30% glycerol
Crystal Properties Matthews coefficient Solvent content 1.53 19.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.443 α = 90 b = 54.676 β = 96.9 c = 34.637 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 2022-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 .8856 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 1.19 36.93 94.27 0.06903 0.07499 0.0289 0.999 12.62 6.5 28352 14.66
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 1.19 1.233 66.45 2.251 2.494 1.053 0.365 0.66 5.3
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 1.19 36.93 1.34 28239 1433 94.25 0.1622 0.1604 0.1581 0.1964 0.1994 random selection 20.28
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 12.1993 f_angle_d 1.4532 f_chiral_restr 0.1057 f_bond_d 0.0188 f_plane_restr 0.0121
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 909 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 6
Software Software Software Name Purpose Blu-Ice data collection PHENIX refinement XDS data reduction BUSTER refinement PHASER phasing XDS data reduction Aimless data scaling