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Crystal structure of Prp8:Aar2 complex: second crystal form at 3.1 Angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SBT PDB ENTRIES 3SBT, 2OG4 experimental model PDB 2OG4 PDB ENTRIES 3SBT, 2OG4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.9 7-9% PEG 8000, 100 MM NA-CITRATE PH 7.9, 50-200 MM AMMONIUM SULFATE
Crystal Properties Matthews coefficient Solvent content 2.75 0.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.42 α = 90 b = 177.841 β = 90 c = 216.601 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS PILATUS 6M 2012-02-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 3.1 137.5 99.9 0.16 6.4 5 97506 2
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 3.1 3.15 100 1.3 1.4 5.2
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 ENTRIES 3SBT, 2OG4 3.1 137.45 84013 4442 99.83 0.22253 0.22022 0.2208 0.26711 0.2676 RANDOM 95.693
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] -2.28 6.95 -4.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.441 r_dihedral_angle_4_deg 22.435 r_dihedral_angle_3_deg 20.135 r_mcangle_it 9.84 r_dihedral_angle_1_deg 7.371 r_mcbond_it 6.118 r_mcbond_other 6.117 r_scbond_it 5.667 r_angle_refined_deg 1.534 r_angle_other_deg 1.042
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.441 r_dihedral_angle_4_deg 22.435 r_dihedral_angle_3_deg 20.135 r_mcangle_it 9.84 r_dihedral_angle_1_deg 7.371 r_mcbond_it 6.118 r_mcbond_other 6.117 r_scbond_it 5.667 r_angle_refined_deg 1.534 r_angle_other_deg 1.042 r_chiral_restr 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.006 r_gen_planes_other 0.004 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28285 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing PHASER phasing SHELXE phasing