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Crystal structure of Chitinase from Vibrio parahaemolyticus at pH6.5
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 6.5 290.15 20% v/v PEG 500* MME, 10 % w/v PEG 20000, 0.06M Magnesium chloride hexahydrate, 0.06M Calcium chloride dihydrate, 0.1M Imidazole, 0.1M MES monohydrate (acid), pH6.5
Crystal Properties Matthews coefficient Solvent content 2.58 52.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.06 α = 90 b = 50.42 β = 126.53 c = 95.33 γ = 90
Symmetry Space Group C 1 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 2024-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.96183 SSRF BL18U1
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 1.7 25.34 99.9 0.075 0.082 0.032 0.999 15.6 6.4 51910 21.46
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.74 1.026 0.469 0.658 1.6
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 1.7 25.34 49312 2594 99.92 0.1975 0.19585 0.2082 0.22891 0.2372 RANDOM 24.419
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] -0.27 0.5 -0.65 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.774 r_dihedral_angle_2_deg 7.149 r_dihedral_angle_1_deg 6.466 r_long_range_B_refined 5.68 r_long_range_B_other 5.642 r_scangle_other 4.947 r_scbond_it 3.354 r_scbond_other 3.353 r_mcangle_it 2.905 r_mcangle_other 2.904
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.774 r_dihedral_angle_2_deg 7.149 r_dihedral_angle_1_deg 6.466 r_long_range_B_refined 5.68 r_long_range_B_other 5.642 r_scangle_other 4.947 r_scbond_it 3.354 r_scbond_other 3.353 r_mcangle_it 2.905 r_mcangle_other 2.904 r_mcbond_it 2.144 r_mcbond_other 2.138 r_angle_refined_deg 1.645 r_angle_other_deg 0.549 r_chiral_restr 0.078 r_gen_planes_refined 0.01 r_bond_refined_d 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 3251 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing