☰ Navigation Tabs
GH5 endo-xyloglucanase from Cellvibrio japonicus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OYC 5OYC.PDB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.5 291 ammonium sulphate, MES buffer
Crystal Properties Matthews coefficient Solvent content 2.35 47.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.343 α = 90 b = 95.83 β = 90 c = 157.208 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) 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 1.9 81.83 100 0.081 0.031 0.998 8.5 7.7 66811
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 1.9 1.94 100 0.592 0.813 7.6
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 (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 5OYC.PDB 1.9 81.83 63393 3299 99.91 0.2374 0.23415 0.2465 0.29997 0.3072 RANDOM 53.356
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] -0.6 7.41 -6.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.291 r_dihedral_angle_4_deg 18.737 r_dihedral_angle_3_deg 14.962 r_long_range_B_other 7.997 r_long_range_B_refined 7.995 r_dihedral_angle_1_deg 7.683 r_scangle_other 6.612 r_mcangle_it 6.601 r_mcangle_other 6.6 r_mcbond_it 5.096
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.291 r_dihedral_angle_4_deg 18.737 r_dihedral_angle_3_deg 14.962 r_long_range_B_other 7.997 r_long_range_B_refined 7.995 r_dihedral_angle_1_deg 7.683 r_scangle_other 6.612 r_mcangle_it 6.601 r_mcangle_other 6.6 r_mcbond_it 5.096 r_mcbond_other 5.094 r_scbond_it 5.073 r_scbond_other 5.073 r_angle_refined_deg 1.933 r_angle_other_deg 1.143 r_chiral_restr 0.133 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5825 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 168
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling REFMAC phasing