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Crystal structure of yeast Brr2 full-lenght in complex with Prp8 Jab1 domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DCA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 0.1 M Tris-HCl pH 7.5,
10.5 % (w/v) PEG 3350,
0.2 M MgCl
Crystal Properties Matthews coefficient Solvent content 3.08 60.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 179.335 α = 90 b = 181.158 β = 90 c = 210.348 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 2015-09-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
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 3.4 50 99.6 0.327 7.1 6.75 94451
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 3.4 3.6 1.56
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 5DCA 3.4 48.72 92351 2100 99.62 0.25301 0.25204 0.2521 0.29629 0.298 RANDOM 94.292
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] 1.73 -3.18 1.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.413 r_dihedral_angle_3_deg 12.201 r_dihedral_angle_4_deg 10.296 r_dihedral_angle_1_deg 4.797 r_long_range_B_refined 4.035 r_long_range_B_other 4.035 r_mcangle_it 2.411 r_mcangle_other 2.411 r_scangle_other 1.425 r_mcbond_it 1.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.413 r_dihedral_angle_3_deg 12.201 r_dihedral_angle_4_deg 10.296 r_dihedral_angle_1_deg 4.797 r_long_range_B_refined 4.035 r_long_range_B_other 4.035 r_mcangle_it 2.411 r_mcangle_other 2.411 r_scangle_other 1.425 r_mcbond_it 1.295 r_mcbond_other 1.295 r_angle_refined_deg 0.937 r_angle_other_deg 0.821 r_scbond_it 0.687 r_scbond_other 0.687 r_chiral_restr 0.053 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 34512 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing