☰ Navigation Tabs
Crystal structure of ricin A chain in complex with inhibitor 9-oxo-4-fluorenecarboxamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RTC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 295 100 mM Tris pH 7.0, 200 mM
Magnesium Chloride, 2.5 M
Sodium Chloride
Crystal Properties Matthews coefficient Solvent content 2.4 49.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.228 α = 90 b = 66.228 β = 90 c = 264.571 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX225HE 2018-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97931 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.54 66.14 100 0.12 0.03 0.99 18.2 25.3 88500
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.54 1.57 99.4 1.2 0.36 0.75 2 11
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1RTC 1.54 66.14 83812 4533 99.95 0.1659 0.1643 0.1953 0.1867 RANDOM 17.912
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] 0.48 0.48 -0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.857 r_dihedral_angle_4_deg 19.965 r_dihedral_angle_3_deg 11.38 r_dihedral_angle_1_deg 5.216 r_angle_refined_deg 1.479 r_angle_other_deg 0.958 r_chiral_restr 0.088 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.857 r_dihedral_angle_4_deg 19.965 r_dihedral_angle_3_deg 11.38 r_dihedral_angle_1_deg 5.216 r_angle_refined_deg 1.479 r_angle_other_deg 0.958 r_chiral_restr 0.088 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4158 Nucleic Acid Atoms Solvent Atoms 764 Heterogen Atoms 117
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction Aimless data scaling PHASER phasing