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Crystal structure of Pisum sativum vicilin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UIK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 0.075M Sodium fluoride, 0.1M Bis-tris propane, 10% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.35 47.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.316 α = 90 b = 52.688 β = 95.193 c = 127.844 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 S 6M 2021-08-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08B1-1 0.98 CLSI 08B1-1
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 3.1 98.104 85.9 0.102 0.142 0.099 0.985 6 3 20422
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 3.1 3.31 0.288 0.401 0.278 0.878 2.1
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 NONE 1UIK 3.1 98.104 20413 1022 84.386 0.19 0.1847 0.1812 0.285 0.2813 46.421
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] -2.951 -2.324 1.555 1.788
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.457 r_dihedral_angle_3_deg 21.108 r_dihedral_angle_4_deg 19.876 r_dihedral_angle_1_deg 8.17 r_lrange_it 7.734 r_lrange_other 7.734 r_mcangle_it 4.982 r_mcangle_other 4.981 r_scangle_it 4.809 r_scangle_other 4.809
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.457 r_dihedral_angle_3_deg 21.108 r_dihedral_angle_4_deg 19.876 r_dihedral_angle_1_deg 8.17 r_lrange_it 7.734 r_lrange_other 7.734 r_mcangle_it 4.982 r_mcangle_other 4.981 r_scangle_it 4.809 r_scangle_other 4.809 r_mcbond_it 3.049 r_mcbond_other 3.049 r_scbond_it 2.862 r_scbond_other 2.862 r_angle_refined_deg 1.487 r_angle_other_deg 1.113 r_nbd_other 0.267 r_symmetry_nbd_refined 0.219 r_nbd_refined 0.216 r_symmetry_xyhbond_nbd_refined 0.198 r_symmetry_nbd_other 0.187 r_xyhbond_nbd_refined 0.178 r_nbtor_refined 0.165 r_symmetry_nbtor_other 0.078 r_symmetry_xyhbond_nbd_other 0.073 r_chiral_restr 0.051 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8488 Nucleic Acid Atoms Solvent Atoms 20 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Coot model building MOLREP phasing DIALS data reduction DIALS data scaling