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Alpha-Galactosaminidase family GH114 from Fusarium solani
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6OJ1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Index A6. 0.1 M Tris 8.5, 2 M ammonium sulphate, with 1 mM TEW, Anderson-Evans polyoxotungstate Jena Bioscience added to the protein prior to crystallisation. Microseed Matrix Seeding
Crystal Properties Matthews coefficient Solvent content 3.06 59.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.569 α = 90 b = 95.569 β = 90 c = 231.428 γ = 120
Symmetry Space Group P 31 2 1
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 EIGER X 16M 2019-06-30 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) R Merge I (Observed) Rrim I (All) 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 1.61 82.77 100 0.113 0.123 0.049 0.999 11.2 12.2 158994 20.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.61 1.64 100 2.346 2.563 1.027 0.461 1 12.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.61 82.765 158854 8055 99.971 0.179 0.1778 0.1778 0.1951 0.1951 29.115
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] 0.315 0.158 0.315 -1.022
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.272 r_dihedral_angle_3_deg 11.068 r_dihedral_angle_2_deg 7.081 r_lrange_it 6.536 r_lrange_other 6.394 r_dihedral_angle_1_deg 6.202 r_scangle_it 3.955 r_scangle_other 3.955 r_scbond_it 2.554 r_scbond_other 2.554
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.272 r_dihedral_angle_3_deg 11.068 r_dihedral_angle_2_deg 7.081 r_lrange_it 6.536 r_lrange_other 6.394 r_dihedral_angle_1_deg 6.202 r_scangle_it 3.955 r_scangle_other 3.955 r_scbond_it 2.554 r_scbond_other 2.554 r_mcangle_it 2.508 r_mcangle_other 2.508 r_angle_refined_deg 1.696 r_mcbond_it 1.686 r_mcbond_other 1.686 r_angle_other_deg 0.652 r_nbd_refined 0.212 r_nbtor_refined 0.178 r_symmetry_nbd_other 0.173 r_xyhbond_nbd_refined 0.154 r_nbd_other 0.145 r_symmetry_xyhbond_nbd_refined 0.129 r_symmetry_nbd_refined 0.116 r_chiral_restr 0.094 r_ncsr_local_group_1 0.083 r_symmetry_nbtor_other 0.076 r_ncsr_local_group_2 0.074 r_ncsr_local_group_3 0.062 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_symmetry_xyhbond_nbd_other 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6785 Nucleic Acid Atoms Solvent Atoms 993 Heterogen Atoms 48
Software Software Software Name Purpose xia2 data reduction XDS data reduction Aimless data scaling MOLREP phasing REFMAC refinement