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Structure of an engineered xylanase Xyl-1 M4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WP4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 295 0.2 M sodium formate, 0.1 M Bis-Tris propane 6.5, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.45 49.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.633 α = 96.91 b = 52.037 β = 102.49 c = 52.232 γ = 107.51
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 Bruker PHOTON III 2022-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 LIQUID ANODE BRUKER METALJET 1.34138
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.3 37.29 99.8 0.0713 15.59 6.52 18177
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.34 98.1 0.229 4.15 3.28
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 2.3 37.29 15202 730 87.49 0.16493 0.16165 0.1711 0.23142 0.2377 RANDOM 22.916
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] 1.63 0.88 0.22 -0.62 -0.55 -1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.453 r_dihedral_angle_3_deg 15.485 r_dihedral_angle_4_deg 13.794 r_dihedral_angle_1_deg 9.433 r_long_range_B_refined 4.413 r_long_range_B_other 4.363 r_scangle_other 3.188 r_mcangle_it 2.277 r_mcangle_other 2.277 r_scbond_it 1.992
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.453 r_dihedral_angle_3_deg 15.485 r_dihedral_angle_4_deg 13.794 r_dihedral_angle_1_deg 9.433 r_long_range_B_refined 4.413 r_long_range_B_other 4.363 r_scangle_other 3.188 r_mcangle_it 2.277 r_mcangle_other 2.277 r_scbond_it 1.992 r_scbond_other 1.985 r_angle_refined_deg 1.503 r_mcbond_it 1.478 r_mcbond_other 1.478 r_angle_other_deg 1.323 r_chiral_restr 0.06 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 2955 Nucleic Acid Atoms Solvent Atoms 226 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement SAINT data scaling SAINT data reduction PHASER phasing