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Structure of Ricin A chain bound with N-(N-(pterin-7-yl)carbonyl-L-serinyl)-L-tryptophan
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 2.69 54.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.827 α = 90 b = 67.827 β = 90 c = 140.673 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 2012-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0 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 1.54 61.1 99.7 0.056 13.3 13.1 49375
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.54 1.57 98.6 0.509 12.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1RTC 1.54 61.1 46787 2500 99.51 0.19874 0.19702 0.23078 0.227 RANDOM 22.78
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] 0.55 0.55 -1.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.618 r_dihedral_angle_4_deg 23.066 r_dihedral_angle_3_deg 16.983 r_scangle_it 6.055 r_dihedral_angle_1_deg 5.905 r_scbond_it 3.969 r_angle_refined_deg 2.806 r_mcangle_it 2.657 r_mcbond_it 1.626 r_chiral_restr 0.266
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.618 r_dihedral_angle_4_deg 23.066 r_dihedral_angle_3_deg 16.983 r_scangle_it 6.055 r_dihedral_angle_1_deg 5.905 r_scbond_it 3.969 r_angle_refined_deg 2.806 r_mcangle_it 2.657 r_mcbond_it 1.626 r_chiral_restr 0.266 r_bond_refined_d 0.028 r_gen_planes_refined 0.016 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2122 Nucleic Acid Atoms Solvent Atoms 221 Heterogen Atoms 54
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