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Mouse acidic mammalian chitinase, catalytic domain in complex with N,N'-diacetylchitobiose at pH 4.91
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8FG5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.91 293.15 11 mg/mL AMCase catalytic domain; 20% w/v PEG 6000; 0.1 M Sodium Acetate pH 4.91; 0.2 M Magnesium Chloride; 29.00 mM GlcNAc2
Crystal Properties Matthews coefficient Solvent content 1.94 36.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.933 α = 90 b = 92.69 β = 90 c = 105.123 γ = 90
Symmetry Space Group P 2 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 2021-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.11578 ALS 8.3.1
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 1.92 105.12 100 0.153 0.167 0.066 0.994 7.7 6.3 53659 13.44
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 1.92 1.95 98.6 0.568 0.617 0.239 0.868 3 6.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.92 70.93 2 53564 2739 99.83 0.1494 0.1472 0.1492 0.1898 0.1909 14.55
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.7772 f_angle_d 0.914 f_chiral_restr 0.0487 f_plane_restr 0.0076 f_bond_d 0.0067
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5880 Nucleic Acid Atoms Solvent Atoms 753 Heterogen Atoms 116
Software Software Software Name Purpose PHENIX refinement xia2 data reduction DIALS data scaling PHASER phasing Coot model building