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Crystal structure of the complex of Ribosome inactivating protein from Momordica balsamina with N-acetyl arginine at 1.7 Angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4F9N
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 2.42 49.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.357 α = 90 b = 130.357 β = 90 c = 40.022 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 2012-05-22 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 1.7 65.2 99.2 0.096 7 27779
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 1.7 1.76 94.7 0.3596 2.1
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 4F9N 1.7 65.18 25027 1395 99.7 0.18862 0.1862 0.1797 0.23594 0.2292 RANDOM 31.999
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] -1.03 -0.51 -1.03 1.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.066 r_dihedral_angle_4_deg 21.636 r_dihedral_angle_3_deg 12.438 r_scangle_it 5.947 r_dihedral_angle_1_deg 5.532 r_scbond_it 3.817 r_mcangle_it 2.334 r_angle_refined_deg 2.123 r_mcbond_it 1.497 r_chiral_restr 0.161
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.066 r_dihedral_angle_4_deg 21.636 r_dihedral_angle_3_deg 12.438 r_scangle_it 5.947 r_dihedral_angle_1_deg 5.532 r_scbond_it 3.817 r_mcangle_it 2.334 r_angle_refined_deg 2.123 r_mcbond_it 1.497 r_chiral_restr 0.161 r_bond_refined_d 0.028 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1910 Nucleic Acid Atoms Solvent Atoms 227 Heterogen Atoms 41
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement AUTOMAR data reduction SCALEPACK data scaling