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Structure of Unliganded MgGH51 a-L-Arabinofuranosidase Crystal Type 2
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 293 10 mg/mL MgGH51 in 10 mM NaOAc pH 5.5, 100 mM NaCl mixed 2:1 with 2.4 M (NH4)2SO4, 0.1 M NaOAc, pH 6, 20% glycerol
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.953 α = 90 b = 125.838 β = 90 c = 161.226 γ = 90
Symmetry Space Group C 2 2 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 EIGER2 X 16M 2019-09-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 1.329 80.743 99.9 0.035 0.999 9.6 8 265496
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 1.33 1.35 98 0.727 0.521 1.1 6.8
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6ZPS 1.329 80.743 265473 13118 99.849 0.131 0.1303 0.1511 0.1463 15.393
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] -0.249 -0.341 0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.039 r_dihedral_angle_4_deg 15.701 r_dihedral_angle_3_deg 11.315 r_dihedral_angle_1_deg 7.043 r_rigid_bond_restr 3.555 r_scangle_it 3.111 r_scangle_other 3.111 r_lrange_it 3.027 r_lrange_other 2.775 r_scbond_it 2.614
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.039 r_dihedral_angle_4_deg 15.701 r_dihedral_angle_3_deg 11.315 r_dihedral_angle_1_deg 7.043 r_rigid_bond_restr 3.555 r_scangle_it 3.111 r_scangle_other 3.111 r_lrange_it 3.027 r_lrange_other 2.775 r_scbond_it 2.614 r_scbond_other 2.614 r_angle_refined_deg 1.931 r_mcangle_it 1.724 r_mcangle_other 1.724 r_angle_other_deg 1.655 r_mcbond_it 1.569 r_mcbond_other 1.505 r_nbd_refined 0.209 r_symmetry_xyhbond_nbd_refined 0.192 r_nbtor_refined 0.18 r_symmetry_nbd_other 0.178 r_nbd_other 0.167 r_xyhbond_nbd_refined 0.136 r_chiral_restr 0.116 r_symmetry_nbd_refined 0.107 r_symmetry_nbtor_other 0.086 r_bond_refined_d 0.014 r_gen_planes_refined 0.013 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4788 Nucleic Acid Atoms Solvent Atoms 719 Heterogen Atoms 229
Software Software Software Name Purpose REFMAC refinement xia2 data reduction DIALS data scaling MOLREP phasing