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Crystal structure of Chitinase 3-like protein 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HJX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 10% PEG8000, 0.5 M NaCl, 0.1 M sodium citrate pH 3.5
Crystal Properties Matthews coefficient Solvent content 2.83 56.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.48 α = 90 b = 122.39 β = 90 c = 137.11 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 PILATUS3 6M 2023-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97853 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.31 50.84 100 0.167 12.2 13.4 81373
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.31 2.37 1.844
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.31 49.97 81297 3961 99.964 0.204 0.2013 0.207 0.2568 0.2612 51.425
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] -1.866 -0.668 2.534
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.878 r_dihedral_angle_3_deg 13.339 r_lrange_other 13.237 r_lrange_it 13.236 r_dihedral_angle_2_deg 10.611 r_scangle_it 8.543 r_scangle_other 8.543 r_mcangle_it 7.623 r_mcangle_other 7.623 r_dihedral_angle_1_deg 7.338
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.878 r_dihedral_angle_3_deg 13.339 r_lrange_other 13.237 r_lrange_it 13.236 r_dihedral_angle_2_deg 10.611 r_scangle_it 8.543 r_scangle_other 8.543 r_mcangle_it 7.623 r_mcangle_other 7.623 r_dihedral_angle_1_deg 7.338 r_scbond_it 5.591 r_scbond_other 5.591 r_mcbond_it 5.201 r_mcbond_other 5.201 r_angle_refined_deg 1.688 r_angle_other_deg 0.594 r_symmetry_xyhbond_nbd_refined 0.371 r_nbd_refined 0.233 r_symmetry_nbd_refined 0.221 r_xyhbond_nbd_refined 0.219 r_symmetry_nbd_other 0.199 r_nbtor_refined 0.189 r_nbd_other 0.179 r_xyhbond_nbd_other 0.092 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.08 r_symmetry_xyhbond_nbd_other 0.029 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11412 Nucleic Acid Atoms Solvent Atoms 252 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-2000 data scaling MOLREP phasing