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Structure of Chitinase 35 from Metschnikowia pulcherrima (MpChit35)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7ZYA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 22% PEG 4000, 100mM magnesium chloride, 100mM sodium acetate pH 4.6
Crystal Properties Matthews coefficient Solvent content 2.16 43.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.582 α = 90 b = 54.85 β = 107.72 c = 97.776 γ = 90
Symmetry Space Group P 1 21 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 PILATUS 6M KB MIRRORS 2023-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979 ALBA XALOC
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 2.55 47.31 99.5 0.184 0.201 0.08 0.985 7.5 6.1 20240
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 2.55 2.66 97.4 0.474 0.521 0.213 0.915 4.7 5.8
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 2.55 47.31 19134 976 98.84 0.18386 0.18108 0.188 0.23817 0.244 RANDOM 24.923
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] -1.15 -2.04 0.03 2.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.009 r_dihedral_angle_1_deg 6.816 r_long_range_B_refined 6.785 r_long_range_B_other 6.784 r_dihedral_angle_2_deg 6.735 r_scangle_other 4.135 r_mcangle_it 2.855 r_mcangle_other 2.854 r_scbond_it 2.542 r_scbond_other 2.541
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.009 r_dihedral_angle_1_deg 6.816 r_long_range_B_refined 6.785 r_long_range_B_other 6.784 r_dihedral_angle_2_deg 6.735 r_scangle_other 4.135 r_mcangle_it 2.855 r_mcangle_other 2.854 r_scbond_it 2.542 r_scbond_other 2.541 r_mcbond_it 1.753 r_mcbond_other 1.747 r_angle_refined_deg 1.436 r_angle_other_deg 0.49 r_chiral_restr 0.066 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 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 4560 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling REFMAC phasing