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Crystal structure of nematode family I chitinase,CeCht1, in complex with dihydropyrrolopyrazol-6-one derivate 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6LDU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 PEG 3350, Bis-tris
Crystal Properties Matthews coefficient Solvent content 2.1 41.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.634 α = 90 b = 67.119 β = 103.657 c = 57.062 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 PILATUS3 6M 2019-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97852 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.85 50 97.6 0.134 13.056 6.3 28692 26.2763693208
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.87 1.9 0.597
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 NONE 6LDU 1.85753436735 40.5551883981 1.36398059093 28682 1998 96.9641649763 0.219184018504 0.216332826894 0.2172 0.257079526656 0.2575 29.8184498671
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 11.836366148 f_angle_d 1.32952498652 f_chiral_restr 0.0790155636842 f_bond_d 0.0119541870201 f_plane_restr 0.00696491910962
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2978 Nucleic Acid Atoms Solvent Atoms 260 Heterogen Atoms 35
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing