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Xylanase from Bacillus circulans mutant E78Q bound to xylotriose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BVV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 5 %v/v PEGSB, 0.071 M Zn Acet, 0.1 M BIS-TRIS, 0.2 M LiSO4
Crystal Properties Matthews coefficient Solvent content 2.64 53.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.32 α = 90 b = 80.32 β = 90 c = 133.48 γ = 90
Symmetry Space Group P 43 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 100 PIXEL DECTRIS PILATUS3 2M 2022-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.965459 ESRF MASSIF-1
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 1.4 43.29 99.6 0.993 10.8 1.8 85922
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 1.4 1.42 99.8 0.606 1.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.41 43.29 76704 4045 95.79 0.18569 0.1843 0.19 0.21145 0.2156 RANDOM 21.14
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] 0.83 0.83 -1.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.375 r_dihedral_angle_1_deg 8.247 r_dihedral_angle_2_deg 7.218 r_long_range_B_refined 5.88 r_long_range_B_other 5.879 r_scangle_other 4.164 r_scbond_it 2.843 r_scbond_other 2.843 r_mcangle_other 2.433 r_mcangle_it 2.432
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.375 r_dihedral_angle_1_deg 8.247 r_dihedral_angle_2_deg 7.218 r_long_range_B_refined 5.88 r_long_range_B_other 5.879 r_scangle_other 4.164 r_scbond_it 2.843 r_scbond_other 2.843 r_mcangle_other 2.433 r_mcangle_it 2.432 r_mcbond_it 1.82 r_mcbond_other 1.82 r_angle_refined_deg 1.518 r_angle_other_deg 0.539 r_chiral_restr 0.073 r_gen_planes_refined 0.01 r_bond_refined_d 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 2896 Nucleic Acid Atoms Solvent Atoms 388 Heterogen Atoms 179
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing