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Crystal structure of Pisum sativum convicilin
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 6 293 0.15M Ammonium Acetate, 25% PEG3350, 0.05M Bis Tris
Crystal Properties Matthews coefficient Solvent content 3.03 59.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 269.155 α = 90 b = 269.155 β = 90 c = 269.155 γ = 90
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 2.7 134.941 99.8 0.127 0.151 0.081 0.995 8.9 5.5 44137
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 2.7 2.81 0.554 0.663 0.359 0.811 5.7
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 2.701 134.941 44134 2246 99.772 0.218 0.2149 0.2127 0.281 0.2811 43.743
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 r_dihedral_angle_2_deg 37.477 r_dihedral_angle_3_deg 21.004 r_dihedral_angle_4_deg 20.163 r_lrange_it 9.667 r_lrange_other 9.666 r_dihedral_angle_1_deg 9.561 r_scangle_it 6.96 r_scangle_other 6.959 r_mcangle_it 6.28 r_mcangle_other 6.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.477 r_dihedral_angle_3_deg 21.004 r_dihedral_angle_4_deg 20.163 r_lrange_it 9.667 r_lrange_other 9.666 r_dihedral_angle_1_deg 9.561 r_scangle_it 6.96 r_scangle_other 6.959 r_mcangle_it 6.28 r_mcangle_other 6.28 r_scbond_it 4.44 r_scbond_other 4.44 r_mcbond_it 4.096 r_mcbond_other 4.096 r_angle_refined_deg 1.768 r_angle_other_deg 1.223 r_nbd_refined 0.224 r_nbd_other 0.198 r_symmetry_nbd_other 0.194 r_symmetry_xyhbond_nbd_refined 0.183 r_symmetry_nbd_refined 0.171 r_nbtor_refined 0.169 r_xyhbond_nbd_refined 0.151 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.075 r_symmetry_xyhbond_nbd_other 0.068 r_xyhbond_nbd_other 0.045 r_bond_refined_d 0.009 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 8329 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Coot model building MOLREP phasing DIALS data reduction DIALS data scaling