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Apo crystal structure of beta-xylosidase from Thermotoga maritima
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 2.55 51.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 179.08 α = 90 b = 98.59 β = 90 c = 100.92 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 1.89 55.402 100 1 49.3 13 143109
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 1.89 1.92 0.39
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 1.89 55.402 143038 7250 99.89 0.195 0.1935 0.1935 0.2262 0.2262 36.454
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] -2.677 2.796 -0.119
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.413 r_dihedral_angle_4_deg 20.093 r_dihedral_angle_3_deg 14.431 r_dihedral_angle_1_deg 6.865 r_lrange_it 6.464 r_scangle_it 5.997 r_scbond_it 4.314 r_mcangle_it 3.401 r_mcbond_it 2.752 r_angle_refined_deg 1.507
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.413 r_dihedral_angle_4_deg 20.093 r_dihedral_angle_3_deg 14.431 r_dihedral_angle_1_deg 6.865 r_lrange_it 6.464 r_scangle_it 5.997 r_scbond_it 4.314 r_mcangle_it 3.401 r_mcbond_it 2.752 r_angle_refined_deg 1.507 r_nbtor_refined 0.314 r_nbd_refined 0.206 r_symmetry_nbd_refined 0.166 r_symmetry_xyhbond_nbd_refined 0.146 r_xyhbond_nbd_refined 0.109 r_chiral_restr 0.097 r_ncsr_local_group_1 0.06 r_bond_refined_d 0.008 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11719 Nucleic Acid Atoms Solvent Atoms 182 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing