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Structure of a xylanase Xyl-1 M4 mutant E175A
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 6.5 295 0.2 M sodium formate, 0.1 M Bis-Tris propane 6.5, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.19 43.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.231 α = 90 b = 137.536 β = 97.66 c = 52.857 γ = 90
Symmetry Space Group P 1 21 1
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 EIGER2 X 9M 2023-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 0.99987 NSRRC TPS 05A
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 1.75 25 95.8 0.042 0.05 0.026 0.997 26 3.8 70638
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 1.75 1.81 90.4 0.123 0.14 0.065 0.988 4.1
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 1.75 23.29 67221 3368 95.44 0.18301 0.18071 0.1891 0.228 0.2339 RANDOM 19.855
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] 1.11 -0.44 -0.05 -0.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.725 r_dihedral_angle_4_deg 15.85 r_dihedral_angle_3_deg 14.875 r_dihedral_angle_1_deg 8.38 r_long_range_B_refined 6.049 r_long_range_B_other 5.918 r_scangle_other 4.438 r_scbond_it 2.981 r_scbond_other 2.98 r_mcangle_it 2.637
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.725 r_dihedral_angle_4_deg 15.85 r_dihedral_angle_3_deg 14.875 r_dihedral_angle_1_deg 8.38 r_long_range_B_refined 6.049 r_long_range_B_other 5.918 r_scangle_other 4.438 r_scbond_it 2.981 r_scbond_other 2.98 r_mcangle_it 2.637 r_mcangle_other 2.637 r_mcbond_it 1.899 r_mcbond_other 1.895 r_angle_refined_deg 1.734 r_angle_other_deg 1.553 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 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 5852 Nucleic Acid Atoms Solvent Atoms 716 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling DENZO data reduction PHASER phasing