☰ Navigation Tabs
Marasmius oreades agglutinin (MOA) activated by manganese (II) and calcium
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, 0.15M sodium acetate, 10 mM MnCl2, 10 mM CaCl2, 12.5% DMSO, 5mM DTT
Crystal Properties Matthews coefficient Solvent content 3.3 63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.569 α = 90 b = 121.569 β = 90 c = 99.584 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 CCD MARMOSAIC 225 mm CCD 2012-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.85051 ESRF ID23-1
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 46.5 97.5 0.061 0.055 0.03 0.998 22.8 3.2 68797
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 1.89 87.3 0.492 0.677 0.463 0.623 2.6
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 46.5 36948 1934 98.747 0.153 0.1517 0.1641 0.1755 0.1864 18.846
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] 0.465 0.232 0.465 -1.507
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.635 r_dihedral_angle_4_deg 14.992 r_dihedral_angle_3_deg 13.432 r_dihedral_angle_1_deg 8.841 r_lrange_it 4.448 r_lrange_other 4.371 r_scangle_it 3.724 r_scangle_other 3.723 r_scbond_it 2.46 r_scbond_other 2.459
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.635 r_dihedral_angle_4_deg 14.992 r_dihedral_angle_3_deg 13.432 r_dihedral_angle_1_deg 8.841 r_lrange_it 4.448 r_lrange_other 4.371 r_scangle_it 3.724 r_scangle_other 3.723 r_scbond_it 2.46 r_scbond_other 2.459 r_mcangle_it 1.978 r_mcangle_other 1.978 r_mcbond_it 1.444 r_mcbond_other 1.441 r_angle_refined_deg 0.954 r_angle_other_deg 0.891 r_symmetry_nbd_refined 0.394 r_nbd_refined 0.214 r_symmetry_metal_ion_refined 0.193 r_symmetry_nbd_other 0.184 r_nbtor_refined 0.171 r_nbd_other 0.152 r_xyhbond_nbd_refined 0.136 r_metal_ion_refined 0.136 r_symmetry_xyhbond_nbd_other 0.13 r_symmetry_xyhbond_nbd_refined 0.111 r_symmetry_nbtor_other 0.107 r_gen_planes_refined 0.041 r_gen_planes_other 0.034 r_bond_refined_d 0.014 r_chiral_restr 0.012 r_bond_other_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2280 Nucleic Acid Atoms Solvent Atoms 212 Heterogen Atoms 128
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing