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Crystal structure of the complex formed between type 1 ribosome inactivating protein and uridine diphosphate at 1.81 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3S9Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.7 298 14% PEG 6000, 0.1M Sodium Phosphate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.43 49.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.964 α = 90 b = 129.964 β = 90 c = 40.445 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 77 CCD MARRESEARCH MIRROR 2013-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.81 50 100 0.063 27.4 22013
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.81 1.87 99.9 0.432 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3S9Q 1.81 38.09 22013 22013 1188 99.97 0.18763 0.18763 0.18581 0.1849 0.22334 0.2207 RANDOM 28.46
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] -0.7 -0.7 -0.7 2.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.228 r_dihedral_angle_4_deg 16.402 r_dihedral_angle_3_deg 12.97 r_long_range_B_refined 5.195 r_long_range_B_other 5.195 r_dihedral_angle_1_deg 4.963 r_scangle_other 1.908 r_mcangle_it 1.604 r_mcangle_other 1.604 r_angle_refined_deg 1.376
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.228 r_dihedral_angle_4_deg 16.402 r_dihedral_angle_3_deg 12.97 r_long_range_B_refined 5.195 r_long_range_B_other 5.195 r_dihedral_angle_1_deg 4.963 r_scangle_other 1.908 r_mcangle_it 1.604 r_mcangle_other 1.604 r_angle_refined_deg 1.376 r_scbond_it 1.131 r_scbond_other 1.129 r_mcbond_it 0.921 r_mcbond_other 0.92 r_angle_other_deg 0.852 r_chiral_restr 0.164 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1911 Nucleic Acid Atoms Solvent Atoms 245 Heterogen Atoms 51
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling