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Structure of Unliganded MgGH51 a-L-Arabinofuranosidase Crystal Type 3
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 1.8 M (NH4)2SO4, 0.1 M NaOAc, pH 5-6, 35% glycerol
Crystal Properties Matthews coefficient Solvent content 3.34 63.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.953 α = 90 b = 83.953 β = 90 c = 256.589 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS PILATUS 2M 2019-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I23 1.3775 Diamond I23
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 1.2 85.53 100 0.011 1 27.2 33 285059
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 1.2 1.22 100 0.43 0.421 1.8 25.1
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 6ZPS 1.2 79.918 284861 14149 99.971 0.121 0.1199 0.12 0.144 0.1442 15.41
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] 0.167 0.167 -0.334
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.969 r_dihedral_angle_4_deg 14.656 r_dihedral_angle_3_deg 11.45 r_rigid_bond_restr 7.532 r_dihedral_angle_1_deg 7.057 r_scbond_it 4.656 r_scbond_other 4.655 r_scangle_it 4.425 r_scangle_other 4.425 r_lrange_it 3.806
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.969 r_dihedral_angle_4_deg 14.656 r_dihedral_angle_3_deg 11.45 r_rigid_bond_restr 7.532 r_dihedral_angle_1_deg 7.057 r_scbond_it 4.656 r_scbond_other 4.655 r_scangle_it 4.425 r_scangle_other 4.425 r_lrange_it 3.806 r_lrange_other 3.681 r_angle_refined_deg 2.073 r_angle_other_deg 1.647 r_mcangle_it 1.327 r_mcangle_other 1.327 r_mcbond_it 1.159 r_mcbond_other 1.153 r_symmetry_xyhbond_nbd_other 0.319 r_nbd_other 0.236 r_nbd_refined 0.233 r_xyhbond_nbd_refined 0.23 r_symmetry_nbd_other 0.19 r_symmetry_xyhbond_nbd_refined 0.185 r_nbtor_refined 0.181 r_symmetry_nbd_refined 0.174 r_chiral_restr 0.13 r_symmetry_nbtor_other 0.09 r_xyhbond_nbd_other 0.035 r_bond_refined_d 0.018 r_gen_planes_refined 0.013 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4788 Nucleic Acid Atoms Solvent Atoms 1082 Heterogen Atoms 264
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing