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Native-crystal structure of three chain non-toxic type II ribosome inactivating protein purified from the seeds of Trichosanthes anguina
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HR6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 0.2M lithium sulfate monohydrate, 0.1M Tris-Hcl, pH8.5, 30% PEG4000
Crystal Properties Matthews coefficient Solvent content 2.77 55.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 171.226 α = 90 b = 171.226 β = 90 c = 75.85 γ = 120
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 MARMOSAIC 225 mm CCD 2015-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.9537 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.9 85.61 100 0.198 0.996 12.6 12.2 28365
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3.06 100 0.648 2.1 11.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4HR6 2.9 85.01 26872 1438 99.87 0.20476 0.20209 0.2058 0.25538 0.2529 RANDOM 59.753
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 -0.28 -0.55 1.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.044 r_dihedral_angle_4_deg 15.308 r_dihedral_angle_3_deg 14.497 r_long_range_B_refined 11.45 r_long_range_B_other 11.45 r_dihedral_angle_1_deg 6.761 r_scangle_other 6.416 r_mcangle_it 6.272 r_mcangle_other 6.271 r_scbond_it 4.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.044 r_dihedral_angle_4_deg 15.308 r_dihedral_angle_3_deg 14.497 r_long_range_B_refined 11.45 r_long_range_B_other 11.45 r_dihedral_angle_1_deg 6.761 r_scangle_other 6.416 r_mcangle_it 6.272 r_mcangle_other 6.271 r_scbond_it 4.05 r_scbond_other 4.05 r_mcbond_it 3.971 r_mcbond_other 3.97 r_angle_refined_deg 1.691 r_angle_other_deg 1.077 r_chiral_restr 0.103 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8009 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing