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Deletion mutant of chitinase MmChi60
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4W5Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 22% (w/v) Poly(acrylic acid sodium salt) average Mw ~5100 Da, 0.02 M MgCl2, 0.1 M HEPES pH 7.5, with N,N',N'', N'''-tetraacetylchitotetraose (NAG4 )
Crystal Properties Matthews coefficient Solvent content 2.27 45.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.499 α = 90 b = 74.086 β = 90 c = 175.569 γ = 90
Symmetry Space Group C 2 2 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 PILATUS 6M focusing mirrors 2019-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9168 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.74 50 97.4 0.085 0.099 0.997 9.97 3.7 33204
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.74 1.85 97.1 0.854 0.99 0.603 1.32 3.9
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 1.743 43.892 33204 1030 97.364 0.178 0.1764 0.1892 0.2223 0.228 24.34
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] -0.521 0.871 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.658 r_dihedral_angle_3_deg 14.42 r_dihedral_angle_2_deg 9.396 r_lrange_it 6.584 r_lrange_other 6.473 r_dihedral_angle_1_deg 6.207 r_scangle_it 4.53 r_scangle_other 4.529 r_scbond_it 3.028 r_mcangle_it 3.018
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.658 r_dihedral_angle_3_deg 14.42 r_dihedral_angle_2_deg 9.396 r_lrange_it 6.584 r_lrange_other 6.473 r_dihedral_angle_1_deg 6.207 r_scangle_it 4.53 r_scangle_other 4.529 r_scbond_it 3.028 r_mcangle_it 3.018 r_mcangle_other 3.017 r_scbond_other 2.964 r_mcbond_it 2.065 r_mcbond_other 2.054 r_angle_refined_deg 1.481 r_angle_other_deg 0.525 r_nbd_refined 0.234 r_symmetry_nbd_refined 0.224 r_nbd_other 0.197 r_symmetry_nbd_other 0.193 r_nbtor_refined 0.185 r_xyhbond_nbd_refined 0.148 r_symmetry_xyhbond_nbd_refined 0.108 r_chiral_restr 0.078 r_symmetry_nbtor_other 0.078 r_metal_ion_refined 0.057 r_symmetry_xyhbond_nbd_other 0.026 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2551 Nucleic Acid Atoms Solvent Atoms 288 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing