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Structure of AraDNJ-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 2.82 56.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.803 α = 90 b = 65.914 β = 90 c = 193.563 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 EIGER2 X 16M 2020-01-22 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) 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 1.7 29.87 99.9 0.028 0.999 15.9 34.5 85172 13.5
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 1.7 1.73 99.4 0.281 0.915 2.1 16.3
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 1.7 29.87 85060 4303 99.894 0.196 0.1946 0.2028 0.2165 0.2252 19.379
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] 4.511 -1.955 -2.556
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.749 r_dihedral_angle_4_deg 18.266 r_dihedral_angle_3_deg 11.878 r_dihedral_angle_1_deg 7.697 r_lrange_it 4.03 r_lrange_other 3.904 r_scangle_it 2.857 r_scangle_other 2.857 r_mcangle_it 2.057 r_mcangle_other 2.056
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.749 r_dihedral_angle_4_deg 18.266 r_dihedral_angle_3_deg 11.878 r_dihedral_angle_1_deg 7.697 r_lrange_it 4.03 r_lrange_other 3.904 r_scangle_it 2.857 r_scangle_other 2.857 r_mcangle_it 2.057 r_mcangle_other 2.056 r_scbond_it 1.984 r_scbond_other 1.984 r_angle_refined_deg 1.666 r_mcbond_it 1.537 r_mcbond_other 1.536 r_angle_other_deg 1.435 r_symmetry_xyhbond_nbd_refined 0.393 r_nbd_refined 0.196 r_symmetry_nbd_other 0.185 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.154 r_symmetry_nbd_refined 0.108 r_chiral_restr_other 0.103 r_nbd_other 0.096 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4767 Nucleic Acid Atoms Solvent Atoms 545 Heterogen Atoms 133
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing