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Crystal structure of native type 1 ribosome inactivating protein from Momordica balsamina at 1.67 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AHA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.7 298 14% PEG6000, 0.1M Sodium Phosphate
, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.43 49.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.181 α = 90 b = 130.181 β = 90 c = 40.292 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 mirrir 2009-07-23 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 1.67 65.09 96.2 0.107 15.2 26840 26840 16.7
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 1.67 1.7 82.3 0.433 2.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1AHA 1.67 65.09 26840 26840 1439 96.24 0.18268 0.18262 0.18159 0.20283 0.1996 RANDOM 20.417
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] -0.71 -0.35 -0.71 1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.646 r_dihedral_angle_4_deg 21.897 r_dihedral_angle_3_deg 11.946 r_dihedral_angle_1_deg 5.24 r_scangle_it 3.956 r_scbond_it 2.573 r_mcangle_it 1.441 r_angle_refined_deg 1.423 r_mcbond_it 0.853 r_chiral_restr 0.094
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.646 r_dihedral_angle_4_deg 21.897 r_dihedral_angle_3_deg 11.946 r_dihedral_angle_1_deg 5.24 r_scangle_it 3.956 r_scbond_it 2.573 r_mcangle_it 1.441 r_angle_refined_deg 1.423 r_mcbond_it 0.853 r_chiral_restr 0.094 r_bond_refined_d 0.015 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1911 Nucleic Acid Atoms Solvent Atoms 277 Heterogen Atoms 26
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling