☰ Navigation Tabs
Crystal structure of beta-xylosidase from Thermotoga maritima in complex with methyl-beta-D-xylopyranoside hydrolysed to xylose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JP0 5JP0, 5Z9S, 5YOT, 3U4A, 5XXL experimental model PDB 5Z9S 5JP0, 5Z9S, 5YOT, 3U4A, 5XXL experimental model PDB 5YOT 5JP0, 5Z9S, 5YOT, 3U4A, 5XXL experimental model PDB 3U4A 5JP0, 5Z9S, 5YOT, 3U4A, 5XXL experimental model PDB 5XXL 5JP0, 5Z9S, 5YOT, 3U4A, 5XXL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.9 293 3% polyethylene glycol 8000, 48% 2-methyl-2,4-pentanediol, 0.1 M sodium cacodylate pH 5.9
Crystal Properties Matthews coefficient Solvent content 2.48 50.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 178.58 α = 90 b = 97.21 β = 90 c = 99.87 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 175 PIXEL DECTRIS EIGER2 XE 16M 2020-10-15 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) 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 1.85 54.923 99.6 0.999 67.8 13.1 147912
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.88 0.433
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5JP0, 5Z9S, 5YOT, 3U4A, 5XXL 1.85 54.923 147781 7499 99.529 0.206 0.2037 0.2037 0.2442 0.2443 45.489
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] -4.742 2.876 1.866
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.308 r_dihedral_angle_4_deg 18.571 r_dihedral_angle_3_deg 14.555 r_dihedral_angle_1_deg 9.491 r_lrange_other 6.778 r_lrange_it 6.776 r_scangle_it 5.699 r_scangle_other 5.698 r_mcangle_it 4.205 r_mcangle_other 4.205
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.308 r_dihedral_angle_4_deg 18.571 r_dihedral_angle_3_deg 14.555 r_dihedral_angle_1_deg 9.491 r_lrange_other 6.778 r_lrange_it 6.776 r_scangle_it 5.699 r_scangle_other 5.698 r_mcangle_it 4.205 r_mcangle_other 4.205 r_scbond_it 4.02 r_scbond_other 4.02 r_mcbond_it 3.245 r_mcbond_other 3.245 r_angle_refined_deg 1.477 r_angle_other_deg 1.271 r_nbd_refined 0.2 r_symmetry_nbd_refined 0.179 r_symmetry_nbd_other 0.177 r_symmetry_xyhbond_nbd_refined 0.167 r_nbtor_refined 0.159 r_xyhbond_nbd_refined 0.13 r_nbd_other 0.13 r_symmetry_nbtor_other 0.075 r_ncsr_local_group_1 0.072 r_chiral_restr 0.067 r_xyhbond_nbd_other 0.066 r_symmetry_xyhbond_nbd_other 0.041 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11783 Nucleic Acid Atoms Solvent Atoms 222 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing