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Crystal structure of Prp8:Aar2 complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SBT 3SBT, 2OG4 experimental model PDB 2OG4 3SBT, 2OG4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.9 293 7-9% PEG8000
0.1M sodium citrate
0.05-0.15M ammonium sulfate , pH 7.9, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.31 46.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.856 α = 90 b = 158.595 β = 90 c = 220.507 γ = 90
Symmetry Space Group C 2 2 21
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 ADSC QUANTUM 315r 2012-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2 48.3 99.9 139972 1.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 100 0.0126 1.5 5
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 (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 3SBT, 2OG4 2 48.3 140035 139972 7046 100 0.201 0.198 0.2024 0.249 0.249 RANDOM 51.52
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] -1.33 2 -0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.158 r_dihedral_angle_4_deg 19.33 r_dihedral_angle_3_deg 16.103 r_dihedral_angle_1_deg 7.761 r_angle_refined_deg 0.947 r_angle_other_deg 0.576 r_chiral_restr 0.065 r_gen_planes_refined 0.011 r_bond_refined_d 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.158 r_dihedral_angle_4_deg 19.33 r_dihedral_angle_3_deg 16.103 r_dihedral_angle_1_deg 7.761 r_angle_refined_deg 0.947 r_angle_other_deg 0.576 r_chiral_restr 0.065 r_gen_planes_refined 0.011 r_bond_refined_d 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14232 Nucleic Acid Atoms Solvent Atoms 670 Heterogen Atoms
Software Software Software Name Purpose MxCuBE data collection MOLREP phasing PHASER phasing SHELXE model building REFMAC refinement XDS data reduction Aimless data scaling