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Crystal structure of Ricin A chain bound with N2-(2-amino-4-oxo-3,4-dihydropteridine-7-carbonyl)glycyl-L-phenylalanyl-N6-((benzyloxy)carbonyl)-L-lysine
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 PEG 2000, Lithium sulfate, Sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.62 53.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.752 α = 90 b = 67.752 β = 90 c = 141.316 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 1.0 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.45 61.093 100 0.031 0.032 0.009 37.9 12.8 59220 59220
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.53 100 0.644 0.644 0.67 0.187 1.2 12.7
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 4HUO 1.45 48.9 56232 2896 99.98 0.223 0.222 0.222 0.2421 0.2417 RANDOM 27.075
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] 0.63 0.63 -1.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.815 r_dihedral_angle_4_deg 16.197 r_dihedral_angle_3_deg 13.257 r_dihedral_angle_1_deg 4.581 r_angle_refined_deg 1.15 r_chiral_restr 0.08 r_bond_refined_d 0.007 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2059 Nucleic Acid Atoms Solvent Atoms 271 Heterogen Atoms 59
Software Software Software Name Purpose XDS data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction