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Structure of a-l-AraCS-Bound MgGH51 a-L-Arabinofuranosidase Crystal Type 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ZPS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 10 mg/mL MgGH51 in 10 mM NaOAc, pH 5.5, 100 mM NaCl mixed 2:1 with 20% PEG 3350, 0.1 M Bis-Tris-HCl, pH 6.5, 0.2 M NaNO3
Crystal Properties Matthews coefficient Solvent content 2.7 54.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 191.63 α = 90 b = 58.09 β = 90 c = 65.71 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS 6M-F 2019-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9119 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.71 58.12 98.8 0.052 0.997 8.7 7.5 79871 21.04
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.71 1.74 98.5 0.694 0.419 6.7
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6ZPS 1.71 55.654 79795 3991 99.413 0.189 0.1867 0.2245 0.217 23.46
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] -0.989 1.04 -0.051
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.363 r_dihedral_angle_4_deg 13.683 r_dihedral_angle_3_deg 12.084 r_dihedral_angle_1_deg 7.601 r_lrange_it 4.033 r_lrange_other 3.981 r_scangle_it 3.17 r_scangle_other 3.17 r_scbond_it 2.258 r_scbond_other 2.255
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.363 r_dihedral_angle_4_deg 13.683 r_dihedral_angle_3_deg 12.084 r_dihedral_angle_1_deg 7.601 r_lrange_it 4.033 r_lrange_other 3.981 r_scangle_it 3.17 r_scangle_other 3.17 r_scbond_it 2.258 r_scbond_other 2.255 r_mcangle_it 2.208 r_mcangle_other 2.208 r_angle_refined_deg 1.746 r_mcbond_it 1.736 r_mcbond_other 1.735 r_angle_other_deg 1.506 r_symmetry_xyhbond_nbd_refined 0.321 r_nbd_refined 0.207 r_symmetry_nbd_other 0.197 r_nbd_other 0.187 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.146 r_symmetry_nbd_refined 0.088 r_symmetry_nbtor_other 0.087 r_chiral_restr 0.078 r_symmetry_xyhbond_nbd_other 0.07 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4763 Nucleic Acid Atoms Solvent Atoms 567 Heterogen Atoms 138
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling MOLREP phasing