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Crystal structure of ricin A chain in complex with inhibitor 4-(2-thienylmethyl)benzoic acid
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 295 200 mM Sodium Acetate, 20%
(w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.7 67.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 168.615 α = 90 b = 168.615 β = 90 c = 54.657 γ = 120
Symmetry Space Group P 63 2 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 2018-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9793 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 2.4 146.02 100 0.14 0.03 0.99 20.9 22.3 18435
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 2.4 2.49 1.54 0.43 0.75 1.9
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1RTC 2.4 146.02 17516 902 99.97 0.187 0.1845 0.1898 0.2352 0.2353 RANDOM 45.035
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] -0.78 -0.39 -0.78 2.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.059 r_dihedral_angle_4_deg 17.005 r_dihedral_angle_3_deg 13.587 r_dihedral_angle_1_deg 5.554 r_angle_refined_deg 1.499 r_angle_other_deg 0.966 r_chiral_restr 0.076 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.059 r_dihedral_angle_4_deg 17.005 r_dihedral_angle_3_deg 13.587 r_dihedral_angle_1_deg 5.554 r_angle_refined_deg 1.499 r_angle_other_deg 0.966 r_chiral_restr 0.076 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2042 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 107
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction Aimless data scaling PHASER phasing