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GH54 a-l-arabinofuranosidase soaked with aziridine inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WD3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 293 2:1 protein:well solution. 0.1 M pH 4.5 sodium acetate buffer, 60% PEG400, 0.3 M (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.232 α = 90 b = 112.232 β = 90 c = 342.73 γ = 120
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 16M 2019-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 1.466 85.54 99.3 0.105 0.109 0.031 0.999 13 12.4 141273
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 1.466 1.491 98.5 2.98 3.13 0.94 0.367 0.7 10.7
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 1WD3 1.466 84.687 141273 6980 99.26 0.158 0.1569 0.1569 0.1791 0.1791 20.664
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] 0.154 0.077 0.154 -0.499
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.439 r_dihedral_angle_4_deg 21.062 r_dihedral_angle_3_deg 10.58 r_dihedral_angle_1_deg 7.567 r_lrange_it 5.344 r_lrange_other 5.074 r_scangle_it 4.3 r_scangle_other 4.299 r_scbond_it 3.195 r_scbond_other 3.194
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.439 r_dihedral_angle_4_deg 21.062 r_dihedral_angle_3_deg 10.58 r_dihedral_angle_1_deg 7.567 r_lrange_it 5.344 r_lrange_other 5.074 r_scangle_it 4.3 r_scangle_other 4.299 r_scbond_it 3.195 r_scbond_other 3.194 r_angle_other_deg 2.577 r_mcangle_it 2.241 r_mcangle_other 2.241 r_angle_refined_deg 1.942 r_mcbond_it 1.737 r_mcbond_other 1.696 r_symmetry_nbd_refined 0.411 r_nbd_other 0.389 r_symmetry_nbd_other 0.222 r_symmetry_xyhbond_nbd_refined 0.221 r_nbd_refined 0.219 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.132 r_chiral_restr 0.097 r_symmetry_nbtor_other 0.089 r_bond_other_d 0.037 r_gen_planes_other 0.018 r_bond_refined_d 0.016 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3578 Nucleic Acid Atoms Solvent Atoms 456 Heterogen Atoms 207
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing