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Engineered endo-1,3-beta-glucanase from Cellulosimicrobium cellulans crystallized at pH 6.2, CcGluECDMH1-E120Q
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ATG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 4.6 298 0.2M (NH4)2SO4, 0.1M NaCH3COO PH4.6, 30% w/v PEGME 2,000
Crystal Properties Matthews coefficient Solvent content 1.85 33.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.821 α = 90 b = 73.821 β = 90 c = 62.59 γ = 120
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 EIGER2 S 9M 2022-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.979145 SSRF BL02U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.76 63.931 99.9 0.137 0.996 10.4 4.1 18292
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.76 1.81 99.7 0.137 0.074 10.4
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 1.76 63.93 18292 922 99.84 0.16317 0.16118 0.1717 0.20339 0.2156 RANDOM 21.742
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] 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.853 r_dihedral_angle_2_deg 10.305 r_dihedral_angle_1_deg 8.255 r_long_range_B_refined 4.838 r_long_range_B_other 4.796 r_scangle_other 3.864 r_scbond_it 2.657 r_scbond_other 2.655 r_mcangle_it 2.58 r_mcangle_other 2.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.853 r_dihedral_angle_2_deg 10.305 r_dihedral_angle_1_deg 8.255 r_long_range_B_refined 4.838 r_long_range_B_other 4.796 r_scangle_other 3.864 r_scbond_it 2.657 r_scbond_other 2.655 r_mcangle_it 2.58 r_mcangle_other 2.58 r_mcbond_other 1.813 r_mcbond_it 1.812 r_angle_refined_deg 1.554 r_angle_other_deg 0.51 r_chiral_restr 0.073 r_gen_planes_refined 0.009 r_bond_refined_d 0.007 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 1848 Nucleic Acid Atoms Solvent Atoms 101 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction Coot model building MOLREP phasing PHENIX refinement autoPROC data scaling autoPROC data reduction