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Coevolved affibody-Z domain pair LL1.c5
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 5 295 2.4 M ammonium Sulfate
0.1 M citric acid pH 5.0
cryoprotected with sodium malonate
Crystal Properties Matthews coefficient Solvent content 1.77 30.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.016 α = 90 b = 42.105 β = 90 c = 140.805 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 EIGER2 XE 16M 2022-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-1 0.77488 SSRL BL12-1
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 1.5 35.8 99.85 0.06605 0.06898 0.01961 0.999 20.23 12 36176 28.59
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 1.5 1.554 99.66 3.09 3.223 0.9039 0.452 0.95 0.95
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5djt 1.5 35.8 1.34 36170 1996 99.86 0.2177 0.2158 0.2507 0.2444 random 39.93
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 12.3764 f_angle_d 0.9215 f_chiral_restr 0.0476 f_bond_d 0.0081 f_plane_restr 0.0073
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1798 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms
Software Software Software Name Purpose Blu-Ice data collection PHENIX refinement XDS data reduction BUSTER refinement PHASER phasing XDS data reduction Aimless data scaling