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Crystal structure of the complex of type I ribosome inactivating protein with 7n-methyl -8-hydroguanosine-5-p-diphosphate at 1.8 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MRW PDB ENTRY 3MRW
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 2.38 48.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.848 α = 90 b = 129.848 β = 90 c = 39.717 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 2010-10-21 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 1.8 37.5 93.2 0.042 33.3 21511 24.6
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 1.8 1.83 62.3 0.27 2.5
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 (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 PDB ENTRY 3MRW 1.8 37.45 21511 20408 1098 93.18 0.18303 0.18084 0.18 0.22597 0.2224 RANDOM 32.621
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] -0.33 -0.16 -0.33 0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.928 r_dihedral_angle_4_deg 15.897 r_dihedral_angle_3_deg 12.999 r_dihedral_angle_1_deg 5.422 r_scangle_it 3.814 r_scbond_it 2.722 r_angle_refined_deg 1.72 r_mcangle_it 1.605 r_mcbond_it 1.05 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.928 r_dihedral_angle_4_deg 15.897 r_dihedral_angle_3_deg 12.999 r_dihedral_angle_1_deg 5.422 r_scangle_it 3.814 r_scbond_it 2.722 r_angle_refined_deg 1.72 r_mcangle_it 1.605 r_mcbond_it 1.05 r_nbtor_refined 0.314 r_nbd_refined 0.212 r_symmetry_vdw_refined 0.199 r_xyhbond_nbd_refined 0.16 r_symmetry_hbond_refined 0.126 r_chiral_restr 0.109 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1911 Nucleic Acid Atoms Solvent Atoms 180 Heterogen Atoms 56
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling