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GH124 cellulase from Ruminiclostridium thermocellum in complex with Mn and cellotriose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XQO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 Tacsimate, PEG 3350, Manganese (II) acetate
Crystal Properties Matthews coefficient Solvent content 2.33 47.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.917 α = 90 b = 73.917 β = 90 c = 74.936 γ = 120
Symmetry Space Group P 32 2 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 S 6M 2016-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.98 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 1.03 74.94 99.9 0.02 15.9 9 116928
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.03 1.06 98.7 0.44 5.3
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2XQO 1.04 64.1 107700 5714 99.9 0.12509 0.12449 0.1243 0.13651 RANDOM 15.83
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] 0.13 0.06 0.13 -0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.083 r_sphericity_free 29.755 r_dihedral_angle_4_deg 18.707 r_dihedral_angle_3_deg 12.023 r_sphericity_bonded 10.088 r_dihedral_angle_1_deg 5.477 r_scangle_other 4.671 r_scbond_it 3.97 r_scbond_other 3.969 r_rigid_bond_restr 3.765
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.083 r_sphericity_free 29.755 r_dihedral_angle_4_deg 18.707 r_dihedral_angle_3_deg 12.023 r_sphericity_bonded 10.088 r_dihedral_angle_1_deg 5.477 r_scangle_other 4.671 r_scbond_it 3.97 r_scbond_other 3.969 r_rigid_bond_restr 3.765 r_long_range_B_refined 3.762 r_long_range_B_other 3.761 r_angle_refined_deg 1.892 r_mcangle_it 1.739 r_mcangle_other 1.738 r_mcbond_it 1.501 r_mcbond_other 1.495 r_angle_other_deg 1.32 r_chiral_restr 0.125 r_bond_refined_d 0.017 r_bond_other_d 0.014 r_gen_planes_refined 0.012 r_gen_planes_other 0.007 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1714 Nucleic Acid Atoms Solvent Atoms 270 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing