☰ Navigation Tabs
Crystal structure of beta-conglutin from Lupinus albus refined to 2.81 A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UIJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 281 40% (v/v) Tacsimate pH 7.0, 50 mM HEPES pH 7.0, 2 mM Spermine, and 2 mM Hexaamine cobalt (III)
Crystal Properties Matthews coefficient Solvent content 3.38 63.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 166.63 α = 90 b = 166.63 β = 90 c = 40.098 γ = 120
Symmetry Space Group P 3 2 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 RIGAKU HyPix-6000HE 2022-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE RIGAKU PhotonJet-S 1.54184
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 2.81 21.77 99.7 0.17 0.182 0.064 0.993 9.1 7.8 15700 55
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 2.81 2.96 100 1.001 1.067 0.366 0.657 2 8.4
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.81 21.767 15686 774 99.771 0.208 0.204 0.2301 0.2772 0.3139 62.202
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] 0.895 0.895 -1.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 20.804 r_dihedral_angle_6_deg 14.932 r_lrange_other 12.243 r_lrange_it 12.238 r_dihedral_angle_2_deg 11.377 r_dihedral_angle_1_deg 8.748 r_scangle_it 7.904 r_scangle_other 7.903 r_mcangle_it 7.673 r_mcangle_other 7.672
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 20.804 r_dihedral_angle_6_deg 14.932 r_lrange_other 12.243 r_lrange_it 12.238 r_dihedral_angle_2_deg 11.377 r_dihedral_angle_1_deg 8.748 r_scangle_it 7.904 r_scangle_other 7.903 r_mcangle_it 7.673 r_mcangle_other 7.672 r_scbond_it 5.08 r_scbond_other 5.079 r_mcbond_it 4.955 r_mcbond_other 4.941 r_angle_refined_deg 1.317 r_angle_other_deg 0.439 r_symmetry_xyhbond_nbd_refined 0.25 r_nbd_other 0.242 r_nbd_refined 0.228 r_symmetry_nbd_refined 0.221 r_symmetry_nbd_other 0.218 r_nbtor_refined 0.188 r_xyhbond_nbd_refined 0.186 r_xyhbond_nbd_other 0.159 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.058 r_symmetry_xyhbond_nbd_other 0.051 r_bond_refined_d 0.005 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 3281 Nucleic Acid Atoms Solvent Atoms 82 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling MOLREP phasing