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Marasmius oreades agglutinin (MOA) in complex with the truncated PVPRAHS synthetic substrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EF2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293.15 0.1 M Cacodylate pH 6.5, 0.2 M Sodium acetate, 22% PEG 8000, 10 mM CaCl2, 5 mM DTT
Crystal Properties Matthews coefficient Solvent content 3.27 62.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.244 α = 90 b = 121.244 β = 90 c = 99.913 γ = 120
Symmetry Space Group P 63 2 2
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 2015-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.972385 ESRF ID29
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 1.56 105 100 0.048 0.166 0.037 0.999 12.3 19.6 61848 23.9
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 1.56 1.59 100 1 1 1 0.362 15
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 3EF2 1.56 51.882 61844 3149 99.981 0.175 0.174 0.1852 0.1993 0.2093 26.788
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] 0.826 0.413 0.826 -2.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.351 r_dihedral_angle_4_deg 21.864 r_dihedral_angle_3_deg 15.391 r_dihedral_angle_1_deg 7.522 r_lrange_it 5.318 r_lrange_other 5.317 r_scangle_it 4.579 r_scangle_other 4.55 r_scbond_it 3.11 r_scbond_other 3.109
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.351 r_dihedral_angle_4_deg 21.864 r_dihedral_angle_3_deg 15.391 r_dihedral_angle_1_deg 7.522 r_lrange_it 5.318 r_lrange_other 5.317 r_scangle_it 4.579 r_scangle_other 4.55 r_scbond_it 3.11 r_scbond_other 3.109 r_mcangle_other 2.947 r_mcangle_it 2.945 r_mcbond_it 2.254 r_mcbond_other 2.179 r_angle_refined_deg 1.824 r_angle_other_deg 1.484 r_symmetry_nbd_refined 0.299 r_nbd_refined 0.217 r_metal_ion_refined 0.178 r_symmetry_nbd_other 0.176 r_nbtor_refined 0.176 r_nbd_other 0.155 r_xyhbond_nbd_refined 0.137 r_symmetry_metal_ion_refined 0.103 r_symmetry_xyhbond_nbd_refined 0.101 r_chiral_restr 0.093 r_symmetry_nbtor_other 0.084 r_symmetry_xyhbond_nbd_other 0.06 r_bond_refined_d 0.013 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 2308 Nucleic Acid Atoms Solvent Atoms 203 Heterogen Atoms 94
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing