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Marasmius oreades agglutinin (MOA) inhibited by cadmium
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, 0.2 M sodium acetate, 1 mM CdCl2, 10 mM CaCl2, 12.5% DMSO, 5 mM DTT
Crystal Properties Matthews coefficient Solvent content 3.3 62.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.752 α = 90 b = 120.752 β = 90 c = 99.541 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 2013-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 2.0664 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 2.1 46.3 92.6 0.196 0.218 0.094 0.995 7.6 5.1 44615
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 2.1 2.15 84.8 1.65 1.85 0.818 0.518
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 2.1 46.3 23997 1204 92.503 0.195 0.193 0.1977 0.2291 0.2336 32.886
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] 1.365 0.683 1.365 -4.428
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.243 r_dihedral_angle_3_deg 13.573 r_dihedral_angle_4_deg 13.248 r_dihedral_angle_1_deg 8.225 r_lrange_it 5.561 r_lrange_other 5.554 r_scangle_it 4.378 r_scangle_other 4.377 r_mcangle_it 3.275 r_mcangle_other 3.274
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.243 r_dihedral_angle_3_deg 13.573 r_dihedral_angle_4_deg 13.248 r_dihedral_angle_1_deg 8.225 r_lrange_it 5.561 r_lrange_other 5.554 r_scangle_it 4.378 r_scangle_other 4.377 r_mcangle_it 3.275 r_mcangle_other 3.274 r_scbond_it 3.003 r_scbond_other 3.002 r_mcbond_it 2.548 r_mcbond_other 2.546 r_angle_refined_deg 1.576 r_angle_other_deg 1.322 r_symmetry_nbd_refined 0.308 r_symmetry_xyhbond_nbd_refined 0.24 r_nbd_refined 0.206 r_symmetry_nbd_other 0.174 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.133 r_nbd_other 0.131 r_symmetry_metal_ion_refined 0.098 r_metal_ion_refined 0.091 r_symmetry_nbtor_other 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_chiral_restr 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2278 Nucleic Acid Atoms Solvent Atoms 101 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing