☰ Navigation Tabs
Crystal structure of GH30 xylanase B from Talaromyces cellulolyticus expressed by Pichia pastoris in complex with aldotriuronic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6IUJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.3 293 PEG 3350, HEPES, magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.49 50.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.251 α = 90 b = 78.7 β = 90 c = 118.418 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 173 PIXEL DECTRIS EIGER X 16M 2019-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.653 33.41 99.41 0.04648 0.05262 0.02424 0.999 15.35 4.5 71087 22.31
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.653 1.712 99.03 0.458 0.5184 0.2389 0.847 2.34 4.5
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6IUJ 1.653 33.41 71087 3554 99.496 0.171 0.1695 0.1897 0.1989 23.318
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] 1.213 0.101 -1.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.378 r_dihedral_angle_4_deg 16.856 r_dihedral_angle_3_deg 12.785 r_dihedral_angle_1_deg 6.222 r_lrange_it 4.876 r_lrange_other 4.77 r_scangle_it 4.262 r_scangle_other 4.261 r_scbond_it 3.257 r_scbond_other 3.257
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.378 r_dihedral_angle_4_deg 16.856 r_dihedral_angle_3_deg 12.785 r_dihedral_angle_1_deg 6.222 r_lrange_it 4.876 r_lrange_other 4.77 r_scangle_it 4.262 r_scangle_other 4.261 r_scbond_it 3.257 r_scbond_other 3.257 r_angle_other_deg 3.179 r_mcangle_it 2.892 r_mcangle_other 2.891 r_mcbond_it 2.281 r_mcbond_other 2.281 r_angle_refined_deg 1.704 r_nbd_other 0.223 r_symmetry_nbd_other 0.214 r_nbd_refined 0.21 r_nbtor_refined 0.181 r_symmetry_nbd_refined 0.174 r_symmetry_xyhbond_nbd_refined 0.15 r_xyhbond_nbd_refined 0.123 r_symmetry_nbtor_other 0.115 r_chiral_restr 0.088 r_bond_other_d 0.036 r_bond_refined_d 0.015 r_gen_planes_other 0.006 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3517 Nucleic Acid Atoms Solvent Atoms 498 Heterogen Atoms 249
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing