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Lotus japonicus CERK6 extracellular domain in complex with chitopentaose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LS2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 292.15 0.2M Potassium sodium tartrate tetrahydrate
0.1M Bis-Tris propane pH 6.5
18% PEG-3350
Crystal Properties Matthews coefficient Solvent content 4.53 72.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.137 α = 90 b = 60.137 β = 90 c = 390.422 γ = 120
Symmetry Space Group P 61 2 2
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 EIGER X 16M 2023-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.97 MAX IV BioMAX
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 2.58 19.68 40.6 0.129 0.132 0.029 0.999 13.4 22 5787 84.07
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 2.58 2.914 6.308 6.45 1.317 0.434
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.58 19.68 1.33 5392 270 37.85 0.2514 0.2504 0.2503 0.2694 0.2706 110.49
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 16.3139 f_angle_d 0.9521 f_chiral_restr 0.0492 f_plane_restr 0.0051 f_bond_d 0.0042
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1524 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 162
Software Software Software Name Purpose PHENIX refinement XDS data reduction STARANISO data scaling PHASER phasing