☰ Navigation Tabs
Crystal structure of Lens culinaris 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 0.01 M Zinc Chloride, 0.1 M Sodium acetate trihydrate, 15% PEG6000, with 20% glycerol as cryoprotectant
Crystal Properties Matthews coefficient Solvent content 2.02 39.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.441 α = 90 b = 92.504 β = 90 c = 143.738 γ = 90
Symmetry Space Group P 21 21 21
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 2021-08-18 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 2.5 143.74 98.6 0.144 0.172 0.093 0.991 9.6 6.2 39945
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 2.5 2.6 0.782 0.939 0.513 0.812 6.2
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 2.5 77.909 39887 2073 98.239 0.204 0.1992 0.1982 0.2839 0.2858 36.052
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] 5.473 -2.584 -2.889
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.872 r_dihedral_angle_3_deg 19.473 r_dihedral_angle_4_deg 19.33 r_dihedral_angle_1_deg 8.321 r_lrange_it 7.777 r_lrange_other 7.777 r_scangle_it 5.272 r_scangle_other 5.272 r_mcangle_it 4.539 r_mcangle_other 4.539
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.872 r_dihedral_angle_3_deg 19.473 r_dihedral_angle_4_deg 19.33 r_dihedral_angle_1_deg 8.321 r_lrange_it 7.777 r_lrange_other 7.777 r_scangle_it 5.272 r_scangle_other 5.272 r_mcangle_it 4.539 r_mcangle_other 4.539 r_scbond_it 3.249 r_scbond_other 3.248 r_mcbond_it 2.874 r_mcbond_other 2.874 r_angle_refined_deg 1.677 r_angle_other_deg 1.204 r_symmetry_xyhbond_nbd_refined 0.23 r_symmetry_nbd_refined 0.229 r_nbd_other 0.226 r_nbd_refined 0.215 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.164 r_xyhbond_nbd_refined 0.149 r_symmetry_xyhbond_nbd_other 0.131 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.068 r_bond_refined_d 0.008 r_gen_planes_refined 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 8688 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling MOLREP phasing Coot model building