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Crystal structure of type I ribosome inactivating protein in complex with maltose at 1.7A 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 2.41 48.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.955 α = 90 b = 129.955 β = 90 c = 40.156 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 2010-05-13 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 37.8 96.7 0.062 33.8 27861 27861 22.2
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 1.73 80.6 0.282 3.3
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 1AHA 1.7 37.8 25578 25578 1359 96.7 0.1829 0.18214 0.17992 0.1771 0.2246 0.2225 RANDOM 27.814
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] -1.25 -0.62 -1.25 1.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.346 r_dihedral_angle_4_deg 16.147 r_dihedral_angle_3_deg 11.107 r_dihedral_angle_1_deg 4.315 r_scangle_it 3.935 r_scbond_it 2.726 r_mcangle_it 1.573 r_angle_refined_deg 1.352 r_mcbond_it 1.047 r_symmetry_hbond_refined 0.604
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.346 r_dihedral_angle_4_deg 16.147 r_dihedral_angle_3_deg 11.107 r_dihedral_angle_1_deg 4.315 r_scangle_it 3.935 r_scbond_it 2.726 r_mcangle_it 1.573 r_angle_refined_deg 1.352 r_mcbond_it 1.047 r_symmetry_hbond_refined 0.604 r_nbtor_refined 0.314 r_symmetry_vdw_refined 0.266 r_nbd_refined 0.217 r_xyhbond_nbd_refined 0.186 r_chiral_restr 0.084 r_bond_refined_d 0.012 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1911 Nucleic Acid Atoms Solvent Atoms 304 Heterogen Atoms 57
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling