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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 Na-acetate pH 5.0, 18% PEG 8000, 0.25 M sodium acetate, 10 mM CaCl2, 5 mM DTT
Crystal Properties Matthews coefficient Solvent content 3.29 62.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.918 α = 90 b = 121.918 β = 90 c = 99.89 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 2014-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97908 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 1.4 46.7 99.7 0.097 0.103 0.033 0.999 10.7 9.7 86228
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.42 93.7 7.367 2.668 8.292 0.367 0.3 9.3
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3EF2 1.4 46.7 86189 4338 99.677 0.187 0.1866 0.203 0.1966 26.914
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] 1.03 0.515 1.03 -3.342
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.92 r_dihedral_angle_4_deg 17.8 r_dihedral_angle_3_deg 13.81 r_dihedral_angle_1_deg 8.3 r_lrange_it 5.058 r_lrange_other 5.057 r_scangle_it 4.033 r_scangle_other 4.033 r_scbond_it 2.736 r_scbond_other 2.733
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.92 r_dihedral_angle_4_deg 17.8 r_dihedral_angle_3_deg 13.81 r_dihedral_angle_1_deg 8.3 r_lrange_it 5.058 r_lrange_other 5.057 r_scangle_it 4.033 r_scangle_other 4.033 r_scbond_it 2.736 r_scbond_other 2.733 r_mcangle_other 2.554 r_mcangle_it 2.553 r_mcbond_it 1.9 r_mcbond_other 1.894 r_angle_refined_deg 0.837 r_angle_other_deg 0.607 r_symmetry_nbd_refined 0.293 r_symmetry_xyhbond_nbd_other 0.25 r_nbd_refined 0.207 r_symmetry_nbd_other 0.184 r_nbtor_refined 0.171 r_nbd_other 0.159 r_xyhbond_nbd_refined 0.132 r_symmetry_metal_ion_refined 0.125 r_metal_ion_refined 0.122 r_symmetry_nbtor_other 0.108 r_symmetry_xyhbond_nbd_refined 0.103 r_gen_planes_refined 0.041 r_gen_planes_other 0.034 r_chiral_restr 0.014 r_bond_refined_d 0.013 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2310 Nucleic Acid Atoms Solvent Atoms 209 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling REFMAC phasing