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Engineered endo-1,3-beta-glucanase from Cellulosimicrobium cellulans crystallized at pH6.2,CcGluECDMH1
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 6.2 298 0.2M (NH4)2SO4 0.1M C2H12AsNaO5 pH6.2 30%PEG8000
Crystal Properties Matthews coefficient Solvent content 1.85 33.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.248 α = 90 b = 73.248 β = 90 c = 62.264 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 1.28 63.931 99.9 0.137 0.996 10.4 4.1 34530
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 1.28 63.43 34530 1780 74.29 0.15441 0.15334 0.1631 0.17495 0.1805 RANDOM 14.71
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] -0.01 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.015 r_dihedral_angle_1_deg 8.39 r_dihedral_angle_2_deg 6.879 r_long_range_B_refined 4.543 r_long_range_B_other 4.511 r_scangle_other 3.585 r_mcangle_other 2.575 r_mcangle_it 2.567 r_scbond_it 2.443 r_scbond_other 2.416
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.015 r_dihedral_angle_1_deg 8.39 r_dihedral_angle_2_deg 6.879 r_long_range_B_refined 4.543 r_long_range_B_other 4.511 r_scangle_other 3.585 r_mcangle_other 2.575 r_mcangle_it 2.567 r_scbond_it 2.443 r_scbond_other 2.416 r_angle_refined_deg 1.9 r_mcbond_it 1.662 r_mcbond_other 1.649 r_angle_other_deg 0.675 r_chiral_restr 0.097 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 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 1844 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement Coot model building PDB_EXTRACT data extraction autoPROC data processing MOLREP phasing autoPROC data reduction autoPROC data scaling