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Crystal structure of yeast full length Brr2 in complex with Prp8 Jab1 domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BGD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.1 M MES-NaOH, pH 6.5, 9 % (w/v) PEG 3350, 0.2 M MgCl2
Crystal Properties Matthews coefficient Solvent content 3.48 64.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.85 α = 90 b = 178.85 β = 90 c = 181.11 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 PSI PILATUS 6M 2015-08-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.9763 PETRA III, EMBL c/o DESY P14 (MX2)
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 2.8 50 98.5 0.105 11.2 3.8 85520 85520
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9
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 4BGD 2.8 50 81271 4257 98.45 0.20484 0.20224 0.205 0.25491 0.2525 RANDOM 101.259
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] 2.03 -4.14 2.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.717 r_dihedral_angle_4_deg 17.691 r_dihedral_angle_3_deg 15.634 r_long_range_B_refined 10 r_long_range_B_other 9.998 r_mcangle_other 6.351 r_mcangle_it 6.35 r_scangle_other 5.871 r_dihedral_angle_1_deg 5.69 r_mcbond_it 3.763
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.717 r_dihedral_angle_4_deg 17.691 r_dihedral_angle_3_deg 15.634 r_long_range_B_refined 10 r_long_range_B_other 9.998 r_mcangle_other 6.351 r_mcangle_it 6.35 r_scangle_other 5.871 r_dihedral_angle_1_deg 5.69 r_mcbond_it 3.763 r_mcbond_other 3.759 r_scbond_it 3.355 r_scbond_other 3.355 r_angle_refined_deg 0.994 r_angle_other_deg 0.706 r_chiral_restr 0.056 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 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 17651 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing