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GH51 a-l-arabinofuranosidase soaked with aziridine inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PZ3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 2:1 protein:well solution. 0.1 M pH 7.5 Tris-HCl buffer, 18% PEG3350, 0.7 M NH4F, 5% 2-propanol
Crystal Properties Matthews coefficient Solvent content 2.73 54.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 178.994 α = 90 b = 178.994 β = 90 c = 100.893 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 2018-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.987 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 29.85 99.5 0.077 0.997 10.8 6.2 235421
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.44 94.5 0.613 0.78 1.5 5.8
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 THROUGHOUT 1PZ3 1.402 29.85 235420 12425 99.512 0.171 0.1702 0.1702 0.1784 0.1784 19.467
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] 0.055 0.027 0.055 -0.177
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.913 r_dihedral_angle_4_deg 19.719 r_dihedral_angle_3_deg 11.714 r_dihedral_angle_1_deg 7.527 r_lrange_it 5.435 r_lrange_other 5.261 r_scangle_it 4.808 r_scangle_other 4.808 r_scbond_it 3.771 r_scbond_other 3.771
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.913 r_dihedral_angle_4_deg 19.719 r_dihedral_angle_3_deg 11.714 r_dihedral_angle_1_deg 7.527 r_lrange_it 5.435 r_lrange_other 5.261 r_scangle_it 4.808 r_scangle_other 4.808 r_scbond_it 3.771 r_scbond_other 3.771 r_mcangle_other 2.999 r_mcangle_it 2.997 r_angle_other_deg 2.537 r_mcbond_it 2.464 r_mcbond_other 2.463 r_angle_refined_deg 2.169 r_symmetry_nbd_refined 0.344 r_nbd_other 0.318 r_nbd_refined 0.226 r_symmetry_nbd_other 0.215 r_symmetry_xyhbond_nbd_refined 0.194 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.15 r_symmetry_xyhbond_nbd_other 0.145 r_chiral_restr 0.128 r_symmetry_nbtor_other 0.078 r_bond_other_d 0.035 r_gen_planes_other 0.026 r_bond_refined_d 0.019 r_gen_planes_refined 0.015
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7747 Nucleic Acid Atoms Solvent Atoms 859 Heterogen Atoms 110
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing