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Marasmius oreades agglutinin (MOA) in complex with the truncated PVVRAHS 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/HCl pH 6.5, 20% PEG 8000, 0.2 M sodium acetate, 10 mM CaCl2, 5 mM DTT
Crystal Properties Matthews coefficient Solvent content 3.3 63.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.155 α = 90 b = 122.155 β = 90 c = 100.02 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 0.97239 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 46.8 99.8 0.145 0.152 0.035 0.999 11.6 19.2 87357
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 1.4 1.42 97.2 5.335 5.489 1.266 0.362 0.362 17.8
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 1.4 46.8 87323 4388 99.8 0.18 0.179 0.1788 0.1978 0.1972 20.883
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] 0.547 0.274 0.547 -1.775
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.253 r_dihedral_angle_3_deg 14.169 r_dihedral_angle_4_deg 14.028 r_dihedral_angle_1_deg 8.229 r_lrange_it 4.381 r_lrange_other 4.38 r_scangle_it 3.377 r_scangle_other 3.377 r_scbond_it 2.237 r_scbond_other 2.229
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.253 r_dihedral_angle_3_deg 14.169 r_dihedral_angle_4_deg 14.028 r_dihedral_angle_1_deg 8.229 r_lrange_it 4.381 r_lrange_other 4.38 r_scangle_it 3.377 r_scangle_other 3.377 r_scbond_it 2.237 r_scbond_other 2.229 r_mcangle_it 2.177 r_mcangle_other 2.177 r_mcbond_it 1.497 r_mcbond_other 1.482 r_angle_refined_deg 0.876 r_angle_other_deg 0.605 r_symmetry_nbd_refined 0.315 r_symmetry_xyhbond_nbd_other 0.252 r_nbd_refined 0.218 r_symmetry_nbd_other 0.182 r_nbtor_refined 0.174 r_nbd_other 0.174 r_metal_ion_refined 0.156 r_symmetry_metal_ion_refined 0.146 r_xyhbond_nbd_refined 0.138 r_symmetry_xyhbond_nbd_refined 0.112 r_symmetry_nbtor_other 0.101 r_gen_planes_refined 0.042 r_gen_planes_other 0.035 r_chiral_restr 0.016 r_bond_refined_d 0.013 r_bond_other_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2305 Nucleic Acid Atoms Solvent Atoms 251 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling REFMAC phasing