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Structure of a-l-AraAZI-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 2.74 55.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.05 α = 90 b = 65.46 β = 90 c = 191.82 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 1.54 61.95 99.7 0.043 0.999 10.6 7.7 110936 18.2
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 1.54 1.57 99.7 0.731 0.505 0.9 6.4
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 1.54 61.95 110838 5515 99.942 0.18 0.1786 0.182 0.2058 0.2099 19.586
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] 1.685 -2.031 0.346
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.883 r_dihedral_angle_4_deg 16.806 r_dihedral_angle_3_deg 11.226 r_dihedral_angle_1_deg 7.548 r_lrange_it 3.998 r_lrange_other 3.812 r_scangle_it 2.978 r_scangle_other 2.978 r_scbond_it 2.126 r_scbond_other 2.126
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.883 r_dihedral_angle_4_deg 16.806 r_dihedral_angle_3_deg 11.226 r_dihedral_angle_1_deg 7.548 r_lrange_it 3.998 r_lrange_other 3.812 r_scangle_it 2.978 r_scangle_other 2.978 r_scbond_it 2.126 r_scbond_other 2.126 r_mcangle_it 1.892 r_mcangle_other 1.892 r_angle_refined_deg 1.756 r_angle_other_deg 1.528 r_mcbond_it 1.416 r_mcbond_other 1.416 r_symmetry_xyhbond_nbd_refined 0.262 r_nbd_refined 0.204 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.179 r_nbd_other 0.139 r_xyhbond_nbd_refined 0.134 r_symmetry_nbd_refined 0.11 r_symmetry_nbtor_other 0.087 r_chiral_restr 0.085 r_bond_refined_d 0.012 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 4760 Nucleic Acid Atoms Solvent Atoms 648 Heterogen Atoms 134
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling MOLREP phasing