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Marasmius oreades agglutinin (MOA) inhibited by zinc
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, 16% PEG 8000, 0.5 M sodium acetate, 50 mM ZnCl2, 10 mM CaCl2, 12.5% DMSO, 5 mM DTT
Crystal Properties Matthews coefficient Solvent content 3.3 62.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.071 α = 90 b = 121.071 β = 90 c = 99.624 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 2013-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.28242 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 1.85 46.4 88.2 0.066 0.073 0.031 0.999 18.2 4.4 64833
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 1.85 1.88 1.437 1.767 0.986 0.489
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 1.85 46.4 35709 1872 94.566 0.208 0.2068 0.2128 0.2347 0.2382 32.884
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] 1.483 0.742 1.483 -4.811
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.305 r_dihedral_angle_4_deg 22.43 r_dihedral_angle_3_deg 14.014 r_dihedral_angle_1_deg 9.377 r_lrange_it 5.199 r_lrange_other 5.192 r_scangle_it 4.479 r_scangle_other 4.477 r_scbond_it 3.388 r_scbond_other 3.387
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.305 r_dihedral_angle_4_deg 22.43 r_dihedral_angle_3_deg 14.014 r_dihedral_angle_1_deg 9.377 r_lrange_it 5.199 r_lrange_other 5.192 r_scangle_it 4.479 r_scangle_other 4.477 r_scbond_it 3.388 r_scbond_other 3.387 r_mcangle_it 3.106 r_mcangle_other 3.106 r_mcbond_other 2.676 r_mcbond_it 2.675 r_angle_refined_deg 0.811 r_angle_other_deg 0.595 r_symmetry_nbd_refined 0.4 r_nbd_other 0.266 r_nbd_refined 0.207 r_symmetry_metal_ion_refined 0.207 r_symmetry_xyhbond_nbd_refined 0.197 r_metal_ion_refined 0.186 r_symmetry_nbd_other 0.183 r_nbtor_refined 0.169 r_xyhbond_nbd_refined 0.135 r_xyhbond_nbd_other 0.123 r_symmetry_nbtor_other 0.105 r_gen_planes_refined 0.041 r_gen_planes_other 0.033 r_bond_refined_d 0.013 r_chiral_restr 0.011 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2278 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms 132
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing