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Structure of Arabinose-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 2.5 50.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.708 α = 90 b = 65.043 β = 90 c = 174.122 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 1.27 65.04 98.5 0.04 0.996 8.7 7.9 176357 11.14
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 1.27 1.29 97.3 0.374 0.764 0.8 7.3
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 1.27 56.544 176207 8652 98.391 0.141 0.1394 0.1383 0.1788 0.1781 14.949
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] -0.47 0.705 -0.235
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.103 r_dihedral_angle_4_deg 16.086 r_dihedral_angle_3_deg 11.616 r_dihedral_angle_1_deg 7.192 r_rigid_bond_restr 3.024 r_lrange_it 2.801 r_scangle_it 2.568 r_scangle_other 2.551 r_lrange_other 2.517 r_scbond_it 2.226
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.103 r_dihedral_angle_4_deg 16.086 r_dihedral_angle_3_deg 11.616 r_dihedral_angle_1_deg 7.192 r_rigid_bond_restr 3.024 r_lrange_it 2.801 r_scangle_it 2.568 r_scangle_other 2.551 r_lrange_other 2.517 r_scbond_it 2.226 r_scbond_other 2.214 r_angle_refined_deg 1.833 r_mcangle_it 1.745 r_mcangle_other 1.745 r_angle_other_deg 1.641 r_mcbond_it 1.5 r_mcbond_other 1.5 r_nbd_refined 0.207 r_nbtor_refined 0.187 r_symmetry_nbd_other 0.184 r_symmetry_xyhbond_nbd_refined 0.146 r_xyhbond_nbd_refined 0.136 r_nbd_other 0.135 r_chiral_restr 0.105 r_symmetry_nbtor_other 0.089 r_symmetry_nbd_refined 0.033 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4775 Nucleic Acid Atoms Solvent Atoms 818 Heterogen Atoms 150
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling MOLREP phasing