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GH5 endo-xyloglucanase from Cellvibrio japonicus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZMR 3ZMR.PDB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.5 291 ammonium sulfate, MES buffer
Crystal Properties Matthews coefficient Solvent content 2.38 48.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.004 α = 90 b = 96.434 β = 90 c = 158.954 γ = 90
Symmetry Space Group P 21 21 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 PILATUS 6M-F 2017-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 1.6 82.45 100 0.06 0.999 11.8 7.8 112339
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 100 0.695 0.699 1 7.9
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3ZMR.PDB 1.6 82.45 106661 5553 99.92 0.14046 0.13717 0.1451 0.20386 0.2087 RANDOM 33.972
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] -0.82 1.81 -0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.934 r_sphericity_free 31.146 r_dihedral_angle_4_deg 18.794 r_sphericity_bonded 15.605 r_dihedral_angle_3_deg 11.264 r_dihedral_angle_1_deg 6.679 r_long_range_B_refined 5.787 r_long_range_B_other 5.787 r_scangle_other 5.725 r_scbond_it 5.034
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.934 r_sphericity_free 31.146 r_dihedral_angle_4_deg 18.794 r_sphericity_bonded 15.605 r_dihedral_angle_3_deg 11.264 r_dihedral_angle_1_deg 6.679 r_long_range_B_refined 5.787 r_long_range_B_other 5.787 r_scangle_other 5.725 r_scbond_it 5.034 r_scbond_other 5.033 r_mcangle_other 4.953 r_mcangle_it 4.95 r_mcbond_it 4.315 r_mcbond_other 4.291 r_rigid_bond_restr 3.828 r_angle_refined_deg 1.687 r_angle_other_deg 1.044 r_chiral_restr 0.105 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 5885 Nucleic Acid Atoms Solvent Atoms 587 Heterogen Atoms 200
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing