☰ Navigation Tabs
Coevolved affibody-Z domain pair LL2.c1
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 2.5 M ammonium sulfate
100 mM HEPES pH 7.0
Cryoprotected with 30% glycerol
Crystal Properties Matthews coefficient Solvent content 1.52 19.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.251 α = 90 b = 54.556 β = 97.64 c = 34.721 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 0.82653 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 1.29 26.46 94.39 0.06021 0.06502 0.02429 0.999 17.31 7.1 22160 15.99
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 1.29 1.336 94.25 1.304 1.404 0.5168 0.824 1.86 7.2
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 1.29 26.46 1.35 22123 1129 94.43 0.2145 0.2133 0.2134 0.2349 0.2352 random selection 22.6
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 14.7356 f_angle_d 1.1608 f_chiral_restr 0.0811 f_bond_d 0.0117 f_plane_restr 0.0084
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 904 Nucleic Acid Atoms Solvent Atoms 97 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