☰ Navigation Tabs
Structure of the human CHI3L1-LZ6 complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8R41
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 0.2 M calcium chloride dihydrate,
0.1 M MES monohydrate, pH 6.0,
20% (w/v) PEG 6,000
Crystal Properties Matthews coefficient Solvent content 2.54 51.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.302 α = 90 b = 122.352 β = 90 c = 136.25 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 EIGER X 9M 2025-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.987 NSLS-II 17-ID-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 2.61 33.83 93.8 0.343 0.381 0.161 0.966 3.7 4.7 52412
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 2.61 2.75 84.3 1.911 2.128 0.911 0.4 4.5
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 2.75 33.83 1.33 45761 1998 95.01 0.1964 0.1944 0.1968 0.239 0.1991
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 16.371 f_angle_d 1.13 f_chiral_restr 0.062 f_plane_restr 0.012 f_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11391 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 264
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PDB_EXTRACT data extraction autoPROC data reduction PHASER phasing