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CjCel5B endo-glucanase bound to CB665 covalent inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TVN 1tvn
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 PS: 10 mg/mL in 5 mM Na-MOPS pH 7.5, 25 mM NaCl
1:1 with WS containing 0.2 M LiCl, 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.13 42.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.49 α = 90 b = 51.83 β = 110.427 c = 64.56 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 EIGER2 XE 16M 2021-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 1.67 32.92 97.5 0.181 0.198 0.08 0.994 6.6 6.1 32027 1
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 1.67 1.7 96.7 2.556 2.784 1.095 0.341 0.8 6.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1tvn 1.67 32.92 32011 1561 97.467 0.188 0.1857 0.2261 0.224 0.05 23.653
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] 0.774 1.597 -1.93 -0.027
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.098 r_dihedral_angle_3_deg 13.331 r_dihedral_angle_4_deg 11.526 r_dihedral_angle_1_deg 7.233 r_lrange_it 3.83 r_lrange_other 3.772 r_scangle_it 3.035 r_scangle_other 3.034 r_scbond_it 2.138 r_scbond_other 2.137
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.098 r_dihedral_angle_3_deg 13.331 r_dihedral_angle_4_deg 11.526 r_dihedral_angle_1_deg 7.233 r_lrange_it 3.83 r_lrange_other 3.772 r_scangle_it 3.035 r_scangle_other 3.034 r_scbond_it 2.138 r_scbond_other 2.137 r_mcangle_it 2.088 r_mcangle_other 2.087 r_mcbond_it 1.594 r_mcbond_other 1.593 r_angle_refined_deg 1.508 r_angle_other_deg 1.435 r_nbd_refined 0.207 r_symmetry_nbd_other 0.182 r_symmetry_nbd_refined 0.179 r_nbtor_refined 0.173 r_symmetry_xyhbond_nbd_refined 0.147 r_nbd_other 0.143 r_xyhbond_nbd_refined 0.127 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.072 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2293 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling MOLREP phasing