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Crystal structure of ricin A chain in complex with inhibitor 5-phenyl-2-thiophenecarboxylic 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 Ammonium Iodide, 20%
(w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.7 67.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 168.355 α = 90 b = 168.355 β = 90 c = 54.834 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 2018-03-07 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 1.99 145.8 100 0.2 0.04 0.99 17.6 24.3 31903
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 1.99 2.04 2.22 0.46 0.81 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 (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 1.99 145.8 30309 1566 99.95 0.1859 0.1843 0.1958 0.218 0.2252 RANDOM 34.023
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] -1.84 -0.92 -1.84 5.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.845 r_dihedral_angle_4_deg 16.62 r_dihedral_angle_3_deg 12.792 r_dihedral_angle_1_deg 5.621 r_angle_refined_deg 1.428 r_angle_other_deg 0.995 r_chiral_restr 0.091 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 36.845 r_dihedral_angle_4_deg 16.62 r_dihedral_angle_3_deg 12.792 r_dihedral_angle_1_deg 5.621 r_angle_refined_deg 1.428 r_angle_other_deg 0.995 r_chiral_restr 0.091 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2060 Nucleic Acid Atoms Solvent Atoms 198 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction Aimless data scaling PHASER phasing