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Structure of Unliganded 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 56.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.98 α = 90 b = 65.801 β = 90 c = 193.12 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 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 1.3 82.28 100 0.035 0.998 6.9 7.8 188207
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 1.3 1.32 99.7 0.422 0.778 6
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 1.3 62.362 188071 9384 99.86 0.18 0.1781 0.1784 0.2174 0.2145 18.808
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] 3.335 -1.622 -1.713
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.442 r_dihedral_angle_4_deg 16.759 r_dihedral_angle_3_deg 12.423 r_dihedral_angle_1_deg 7.365 r_rigid_bond_restr 3.843 r_scangle_other 2.801 r_scangle_it 2.797 r_lrange_it 2.673 r_scbond_it 2.622 r_scbond_other 2.622
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.442 r_dihedral_angle_4_deg 16.759 r_dihedral_angle_3_deg 12.423 r_dihedral_angle_1_deg 7.365 r_rigid_bond_restr 3.843 r_scangle_other 2.801 r_scangle_it 2.797 r_lrange_it 2.673 r_scbond_it 2.622 r_scbond_other 2.622 r_lrange_other 2.552 r_mcangle_other 2.084 r_mcangle_it 2.077 r_angle_refined_deg 1.899 r_mcbond_it 1.834 r_mcbond_other 1.818 r_angle_other_deg 1.593 r_nbd_refined 0.202 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.18 r_symmetry_xyhbond_nbd_refined 0.156 r_xyhbond_nbd_refined 0.136 r_chiral_restr 0.118 r_nbd_other 0.114 r_symmetry_xyhbond_nbd_other 0.095 r_symmetry_nbtor_other 0.087 r_symmetry_nbd_refined 0.049 r_bond_refined_d 0.016 r_gen_planes_refined 0.015 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4769 Nucleic Acid Atoms Solvent Atoms 643 Heterogen Atoms 124
Software Software Software Name Purpose REFMAC refinement xia2 data reduction DIALS data scaling MOLREP phasing