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Native structure of IRIP, a type I ribosome inactivating protein from Iris hollandica var. at 1.25 A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1M2T PDB ENTRY 1M2T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 1.9M ammonium sulfate in 20% w/v glycerol, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.33 47.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.879 α = 90 b = 84.809 β = 97.67 c = 69.08 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MAR CCD 165 mm 2007-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.81480 EMBL/DESY, HAMBURG X11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.25 30 99.8 0.051 0.447 25.6 4.4 157596 2.6 17.62
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.247 1.28 98 0.649 0.45 2.67 4.4 7666
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 PDB ENTRY 1M2T 1.25 30 157596 7893 99.6 0.16931 0.16846 0.1687 0.18542 0.185 RANDOM 17.883
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] 0.28 0.71 -0.11 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.805 r_dihedral_angle_4_deg 17.331 r_dihedral_angle_3_deg 11.455 r_dihedral_angle_1_deg 5.7 r_scangle_it 2.307 r_scbond_it 1.47 r_angle_refined_deg 1.185 r_mcangle_it 0.987 r_mcbond_it 0.52 r_chiral_restr 0.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.805 r_dihedral_angle_4_deg 17.331 r_dihedral_angle_3_deg 11.455 r_dihedral_angle_1_deg 5.7 r_scangle_it 2.307 r_scbond_it 1.47 r_angle_refined_deg 1.185 r_mcangle_it 0.987 r_mcbond_it 0.52 r_chiral_restr 0.078 r_bond_refined_d 0.007 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3990 Nucleic Acid Atoms Solvent Atoms 756 Heterogen Atoms 109
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling