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X-ray structure of the single chain monellin derivative MNEI
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 209U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 30-33% PEG4K, 0.1 M sodium acetate buffer pH 4.5 and 0.2 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.02 39.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.65 α = 105.995 b = 38.97 β = 109.521 c = 44.13 γ = 103.361
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 2021-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 0.96 ELETTRA 11.2C
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 1.19 38.39 92.7 0.037 0.044 0.024 0.999 14.2 3.4 52760
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 1.19 1.21 85.4 0.679 0.815 0.443 0.726 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 1.19 38.39 50006 2465 87.278 0.218 0.2161 0.2562 0.2817 16.7
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] -0.007 -0.027 0.036 0.036 -0.023 -0.017
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.329 r_dihedral_angle_3_deg 14.193 r_dihedral_angle_4_deg 11.882 r_dihedral_angle_1_deg 6.532 r_lrange_it 5.536 r_lrange_other 5.535 r_scangle_it 3.403 r_scangle_other 3.402 r_mcangle_it 2.287 r_mcangle_other 2.287
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.329 r_dihedral_angle_3_deg 14.193 r_dihedral_angle_4_deg 11.882 r_dihedral_angle_1_deg 6.532 r_lrange_it 5.536 r_lrange_other 5.535 r_scangle_it 3.403 r_scangle_other 3.402 r_mcangle_it 2.287 r_mcangle_other 2.287 r_scbond_it 2.19 r_scbond_other 2.189 r_angle_refined_deg 1.768 r_mcbond_it 1.514 r_mcbond_other 1.505 r_angle_other_deg 1.385 r_nbd_other 0.248 r_symmetry_nbd_refined 0.233 r_nbd_refined 0.223 r_metal_ion_refined 0.199 r_symmetry_nbd_other 0.193 r_xyhbond_nbd_refined 0.186 r_nbtor_refined 0.181 r_symmetry_xyhbond_nbd_refined 0.156 r_chiral_restr 0.079 r_symmetry_nbtor_other 0.079 r_symmetry_xyhbond_nbd_other 0.045 r_xyhbond_nbd_other 0.031 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1604 Nucleic Acid Atoms Solvent Atoms 263 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing