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Crystal structure of Ricin A chain bound with N2-(2-amino-4-oxo-3,4-dihydropteridine-7-carbonyl)glycyl-L-tyrosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HUO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 296 PEG2000, Lithium sulfate, Sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.58 52.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.803 α = 90 b = 67.803 β = 90 c = 141.38 γ = 90
Symmetry Space Group P 41 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 95 PIXEL DECTRIS PILATUS 6M 2019-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.6 48.93 99.2 0.042 0.012 1 35.6 13 43942
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.6 1.69 98.3 0.801 0.214 0.912 13.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.6 48.93 41706 2191 98.94 0.21563 0.21471 0.2149 0.23235 0.2319 RANDOM 26.051
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] 0.57 0.57 -1.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.217 r_dihedral_angle_4_deg 20.915 r_dihedral_angle_3_deg 13.325 r_dihedral_angle_1_deg 4.85 r_long_range_B_refined 4.461 r_mcangle_it 1.409 r_scbond_it 1.219 r_angle_refined_deg 1.142 r_mcbond_it 0.843 r_chiral_restr 0.079
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.217 r_dihedral_angle_4_deg 20.915 r_dihedral_angle_3_deg 13.325 r_dihedral_angle_1_deg 4.85 r_long_range_B_refined 4.461 r_mcangle_it 1.409 r_scbond_it 1.219 r_angle_refined_deg 1.142 r_mcbond_it 0.843 r_chiral_restr 0.079 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2035 Nucleic Acid Atoms Solvent Atoms 235 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement SCALA data scaling XDS data reduction MOLREP phasing