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Unheat-treated beta-conglycinin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IPJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293.15 11% PEG4000, 0.1M Sodium Chloride, 0.1M Tris
Crystal Properties Matthews coefficient Solvent content 2.69 54.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.019 α = 90 b = 63.097 β = 91.31 c = 121.85 γ = 90
Symmetry Space Group P 1 21 1
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 PILATUS3 6M 2023-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97918 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.78 42.11 99.67 0.964 4.2 1.34 66251 29.55
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.78 2.82 0.964
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.78 42.11 1.34 66251 3830 99.35 0.249 0.2443 0.2445 0.3248 0.3236 40.77
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 6.4641 f_angle_d 1.1261 f_chiral_restr 0.0612 f_plane_restr 0.0094 f_bond_d 0.0089
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8985 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms
Software Software Software Name Purpose HKL-3000 data scaling HKL-3000 data reduction PDB_EXTRACT data extraction PHASER phasing PHENIX refinement