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Crystal Structure of chitinase (E167Q) from the carnivorous plant Drosera adelae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 15% PEG 8000
40% 2-Propanol
0.1 M Imidazole pH 6.5
Crystal Properties Matthews coefficient Solvent content 1.89 34.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.12 α = 90 b = 63.247 β = 90 c = 72.894 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 2023-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.57 47.77 93.7 0.029 0.032 0.013 33.7 5.9 26673
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 1.57 1.6 60.4 0.404 0.472 0.237 0.873 2.7 3.5
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 (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 THROUGHOUT 1.57 47.77 25329 1303 93.33 0.20358 0.20196 0.2098 0.23438 0.2388 RANDOM 22.243
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] 0.02 -0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.151 r_dihedral_angle_4_deg 18.193 r_dihedral_angle_3_deg 11.767 r_dihedral_angle_1_deg 6.303 r_long_range_B_refined 4.887 r_long_range_B_other 4.83 r_scangle_other 3.624 r_mcangle_it 2.799 r_mcangle_other 2.798 r_scbond_it 2.525
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.151 r_dihedral_angle_4_deg 18.193 r_dihedral_angle_3_deg 11.767 r_dihedral_angle_1_deg 6.303 r_long_range_B_refined 4.887 r_long_range_B_other 4.83 r_scangle_other 3.624 r_mcangle_it 2.799 r_mcangle_other 2.798 r_scbond_it 2.525 r_scbond_other 2.523 r_mcbond_it 2.03 r_mcbond_other 2.03 r_angle_refined_deg 1.597 r_angle_other_deg 1.515 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1857 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing