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CjCel5C endo-glucanase bound to CB396 covalent inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HTY 4HTY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 PS: 12 mg/mL in 20 mM MOPS 7.5, 50 mM NaCl
1.5:1 with WS containing 30% MPD, 6% PEG4000, with seeding from higher [PEG] crystals. Soaked with ligand overnight.
Crystal Properties Matthews coefficient Solvent content 2.67 53.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.441 α = 90 b = 176.159 β = 90 c = 115.701 γ = 90
Symmetry Space Group C 2 2 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 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 2.7 102.72 93.8 0.352 0.369 0.108 0.989 6.8 11.6 33580 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 2.7 2.75 99 2.98 3.131 0.948 0.377 10.6
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4HTY 2.701 102.72 33473 1688 93.492 0.187 0.1851 0.1861 0.2243 0.2243 0.05 47.418
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] -3.298 1.679 1.618
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.27 r_dihedral_angle_6_deg 15.095 r_dihedral_angle_2_deg 10.177 r_dihedral_angle_1_deg 8.914 r_lrange_it 7.084 r_lrange_other 7.083 r_mcangle_it 5.708 r_mcangle_other 5.708 r_scangle_it 5.395 r_scangle_other 5.395
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.27 r_dihedral_angle_6_deg 15.095 r_dihedral_angle_2_deg 10.177 r_dihedral_angle_1_deg 8.914 r_lrange_it 7.084 r_lrange_other 7.083 r_mcangle_it 5.708 r_mcangle_other 5.708 r_scangle_it 5.395 r_scangle_other 5.395 r_mcbond_it 3.855 r_mcbond_other 3.854 r_scbond_it 3.654 r_scbond_other 3.654 r_angle_refined_deg 1.317 r_angle_other_deg 0.447 r_symmetry_xyhbond_nbd_refined 0.26 r_nbd_other 0.22 r_nbd_refined 0.219 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.184 r_symmetry_nbd_refined 0.176 r_xyhbond_nbd_refined 0.174 r_symmetry_nbtor_other 0.08 r_ncsr_local_group_3 0.061 r_ncsr_local_group_1 0.06 r_chiral_restr 0.059 r_ncsr_local_group_2 0.055 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8043 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing