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Crystal Structure of chitinase from the carnivorous plant Drosera adelae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9JTP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.8 M K2HPO4
0.8 M NaH2PO4
0.1 M HEPES pH7.5
Crystal Properties Matthews coefficient Solvent content 2.83 56.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.222 α = 90 b = 73.222 β = 90 c = 192.998 γ = 120
Symmetry Space Group P 32 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 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) 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 1.73 48.25 100 0.052 0.055 0.018 1 26.5 9.5 63657
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 1.73 1.76 100 0.787 0.84 0.292 0.773 2.2
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 1.73 38.43 60440 3145 99.97 0.20929 0.20776 0.2177 0.2382 0.2404 RANDOM 27.509
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] 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.057 r_long_range_B_other 19.414 r_long_range_B_refined 19.356 r_dihedral_angle_4_deg 15.38 r_dihedral_angle_3_deg 12.386 r_dihedral_angle_1_deg 6.067 r_scangle_other 4.604 r_scbond_it 3.336 r_scbond_other 3.335 r_mcangle_it 2.758
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.057 r_long_range_B_other 19.414 r_long_range_B_refined 19.356 r_dihedral_angle_4_deg 15.38 r_dihedral_angle_3_deg 12.386 r_dihedral_angle_1_deg 6.067 r_scangle_other 4.604 r_scbond_it 3.336 r_scbond_other 3.335 r_mcangle_it 2.758 r_mcangle_other 2.757 r_mcbond_it 2.269 r_mcbond_other 2.269 r_angle_refined_deg 1.75 r_angle_other_deg 1.511 r_chiral_restr 0.091 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 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 3714 Nucleic Acid Atoms Solvent Atoms 537 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing