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GH54 a-l-arabinofuranosidase soaked with cyclic sulfate 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 4 34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.136 α = 90 b = 111.136 β = 90 c = 342.742 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 1.859 84.059 100 0.128 0.133 0.039 0.999 10.2 12.1 68786
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 1.86 1.89 100 5.32 5.54 1.53 0.44 0.5 12.8
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 FREE R-VALUE 1WD3 1.859 84.059 68786 3338 99.73 0.183 0.1817 0.1818 0.215 0.2155 40.242
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] 0.885 0.443 0.885 -2.872
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.2 r_dihedral_angle_4_deg 21.509 r_dihedral_angle_3_deg 11.758 r_dihedral_angle_1_deg 8.225 r_lrange_it 5.61 r_lrange_other 5.591 r_scangle_it 5.198 r_scangle_other 5.197 r_scbond_it 4.036 r_scbond_other 4.035
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.2 r_dihedral_angle_4_deg 21.509 r_dihedral_angle_3_deg 11.758 r_dihedral_angle_1_deg 8.225 r_lrange_it 5.61 r_lrange_other 5.591 r_scangle_it 5.198 r_scangle_other 5.197 r_scbond_it 4.036 r_scbond_other 4.035 r_mcangle_other 3.688 r_mcangle_it 3.686 r_mcbond_it 3.102 r_mcbond_other 3.059 r_angle_refined_deg 1.768 r_angle_other_deg 1.463 r_symmetry_nbd_refined 0.311 r_nbd_other 0.216 r_nbd_refined 0.196 r_symmetry_nbd_other 0.18 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.129 r_symmetry_xyhbond_nbd_refined 0.122 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.076 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3568 Nucleic Acid Atoms Solvent Atoms 235 Heterogen Atoms 131
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing