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Coevolved affibody-Z domain pair LL2.c3
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 7 295 2.4 M Ammonium sulfate
0.1M HEPES pH 7.0
Cryoprotected with 30% glycerol
Crystal Properties Matthews coefficient Solvent content 1.6 23.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.403 α = 90 b = 54.259 β = 94.41 c = 68.601 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 0.88557 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 1.35 38 95.84 0.1129 0.1224 0.0467 0.997 8.93 6.8 41323 17.62
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 1.35 1.398 93.56 3.679 3.989 1.522 0.172 0.76 93.56
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 1.35 38 1.34 41193 1640 95.85 0.1763 0.1754 0.1759 0.1981 0.199 random selection 23.47
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 13.2621 f_angle_d 1.3135 f_chiral_restr 0.0762 f_bond_d 0.014 f_plane_restr 0.0095
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1820 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms 27
Software Software Software Name Purpose Blu-Ice data collection PHENIX refinement XDS data reduction BUSTER refinement PHENIX phasing XDS data reduction Aimless data scaling