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Crystal structure of Ribosome inactivating protein from Momordica balsamina complexed with Polyethylene glycol at 1.90 Angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4G2X
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 2.33 47.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.411 α = 90 b = 130.411 β = 90 c = 38.627 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 2012-11-17 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 1.9 65.21 100 0.066 50.5 19298 19298
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 1.9 1.93 100 2.6
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 4G2X 1.9 65.21 18306 988 99.98 0.18229 0.17957 0.1789 0.23267 0.233 RANDOM 39.739
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] -2.31 -1.15 -2.31 3.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.683 r_dihedral_angle_4_deg 20.708 r_dihedral_angle_3_deg 14.869 r_dihedral_angle_1_deg 5.407 r_scangle_it 5.351 r_scbond_it 3.419 r_mcangle_it 1.985 r_angle_refined_deg 1.805 r_mcbond_it 1.174 r_chiral_restr 0.139
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.683 r_dihedral_angle_4_deg 20.708 r_dihedral_angle_3_deg 14.869 r_dihedral_angle_1_deg 5.407 r_scangle_it 5.351 r_scbond_it 3.419 r_mcangle_it 1.985 r_angle_refined_deg 1.805 r_mcbond_it 1.174 r_chiral_restr 0.139 r_bond_refined_d 0.024 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1910 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 27
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling