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Crystal structure of GH30 xylanase B from Talaromyces cellulolyticus expressed by Pichia pastoris
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 7.5 293 PEG 3350, HEPES, magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.48 50.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.337 α = 90 b = 78.765 β = 90 c = 117.839 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 EIGER X 16M 2019-01-24 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) 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 1.601 43.144 99.59 0.09292 0.03888 0.996 11.8 6.7 78001 21.05
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.601 1.658 96.61 0.8014 0.3322 0.66 2 6.8
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 FREE R-VALUE 6IUJ 1.601 43.14 78001 3900 99.602 0.174 0.1723 0.183 0.1984 0.2073 22.058
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] 0.521 0.119 -0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.739 r_dihedral_angle_4_deg 17.278 r_dihedral_angle_3_deg 11.781 r_dihedral_angle_1_deg 6.712 r_lrange_it 4.717 r_lrange_other 4.574 r_scangle_it 3.228 r_scangle_other 3.228 r_mcangle_other 2.282 r_mcangle_it 2.281
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.739 r_dihedral_angle_4_deg 17.278 r_dihedral_angle_3_deg 11.781 r_dihedral_angle_1_deg 6.712 r_lrange_it 4.717 r_lrange_other 4.574 r_scangle_it 3.228 r_scangle_other 3.228 r_mcangle_other 2.282 r_mcangle_it 2.281 r_scbond_it 2.091 r_scbond_other 2.091 r_angle_refined_deg 1.483 r_mcbond_it 1.452 r_mcbond_other 1.448 r_angle_other_deg 1.431 r_nbd_refined 0.199 r_symmetry_nbd_other 0.18 r_symmetry_xyhbond_nbd_refined 0.175 r_nbtor_refined 0.167 r_nbd_other 0.152 r_xyhbond_nbd_refined 0.127 r_symmetry_nbtor_other 0.113 r_chiral_restr 0.07 r_symmetry_nbd_refined 0.058 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3500 Nucleic Acid Atoms Solvent Atoms 410 Heterogen Atoms 187
Software Software Software Name Purpose REFMAC refinement XDS data scaling MOLREP phasing Coot model building XDS data reduction