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Crystal structure of ricin A chain in complex with 5-mesitylthiophene-2-carboxylic 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 6.5 295 50 mM Bis-Tris pH 6.5, 50 mM Ammonium Sulfate, 30 %(v/v) Pentaerythritol Ethoxylate (15/4 EO/OH)
Crystal Properties Matthews coefficient Solvent content 2.3 46.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.407 α = 90 b = 56.496 β = 93.34 c = 126.903 γ = 90
Symmetry Space Group P 1 21 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 CCD RAYONIX MX225HE 2021-02-24 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) 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 1.65 126.69 97.7 0.03 0.99 11.8 3.7 63861
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.68 0.59 0.55 1.1
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 1.65 126.69 60555 3284 97.46 0.2109 0.2095 0.2172 0.2375 0.244 RANDOM 29.999
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] 1.43 -0.03 -1.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.034 r_dihedral_angle_4_deg 20.269 r_dihedral_angle_3_deg 13.57 r_dihedral_angle_1_deg 6.037 r_angle_refined_deg 1.465 r_angle_other_deg 1.352 r_chiral_restr 0.066 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.034 r_dihedral_angle_4_deg 20.269 r_dihedral_angle_3_deg 13.57 r_dihedral_angle_1_deg 6.037 r_angle_refined_deg 1.465 r_angle_other_deg 1.352 r_chiral_restr 0.066 r_bond_refined_d 0.008 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 4065 Nucleic Acid Atoms Solvent Atoms 246 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction Aimless data scaling PHASER phasing