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Structure of Ricin A chain bound with N-(N-(pterin-7-yl)carbonylglycyl)-L-phenylalanine
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 5 277 1.3 M Ammonium sulfate, 0.1 M sodium malonate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.72 54.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.999 α = 90 b = 67.999 β = 90 c = 140.692 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 100 CCD ADSC QUANTUM 315 2011-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 0.9202 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.52 61.22 99.8 0.098 7.3 13.8 51425
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.52 1.55 100 13.3 2542
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 1.52 61.22 50859 2587 98.88 0.2025 0.2011 0.1987 0.2304 0.227 RANDOM 23.2333
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] 0.59 0.59 -1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.888 r_dihedral_angle_4_deg 19.386 r_dihedral_angle_3_deg 14.267 r_dihedral_angle_1_deg 5.463 r_scangle_it 5.4 r_scbond_it 3.482 r_mcangle_it 2.358 r_angle_refined_deg 2.212 r_angle_other_deg 1.59 r_mcbond_it 1.482
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.888 r_dihedral_angle_4_deg 19.386 r_dihedral_angle_3_deg 14.267 r_dihedral_angle_1_deg 5.463 r_scangle_it 5.4 r_scbond_it 3.482 r_mcangle_it 2.358 r_angle_refined_deg 2.212 r_angle_other_deg 1.59 r_mcbond_it 1.482 r_chiral_restr 0.162 r_bond_refined_d 0.027 r_gen_planes_refined 0.016 r_gen_planes_other 0.008 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2078 Nucleic Acid Atoms Solvent Atoms 397 Heterogen Atoms 30
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction BOS data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing