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Structure of the Shq1-Cbf5-Nop10-Gar1 complex from Saccharomyces cerevisiae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3UAH 3UAH, 3U28 experimental model PDB 3U28 3UAH, 3U28
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 297 0.1M Bis-Tris, 20%(w/v) polyethylene glycol monomethyl ether 5000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 3.24 62.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.995 α = 90 b = 100.995 β = 90 c = 272.329 γ = 90
Symmetry Space Group P 43 21 2
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 2011-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9789 SSRF BL17U
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 3.06 50 99.9 0.067 58.4 14.1 27487
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 3.06 3.11 100 0.684 5.6 14.7
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 3UAH, 3U28 3.06 20 25934 1370 99.9 0.22162 0.21886 0.209 0.27526 0.2615 RANDOM 100.637
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] 1.62 1.62 -3.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.115 r_dihedral_angle_3_deg 19.102 r_dihedral_angle_4_deg 16.606 r_dihedral_angle_1_deg 5.933 r_scangle_it 1.603 r_angle_refined_deg 1.21 r_scbond_it 0.903 r_mcangle_it 0.728 r_mcbond_it 0.379 r_chiral_restr 0.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.115 r_dihedral_angle_3_deg 19.102 r_dihedral_angle_4_deg 16.606 r_dihedral_angle_1_deg 5.933 r_scangle_it 1.603 r_angle_refined_deg 1.21 r_scbond_it 0.903 r_mcangle_it 0.728 r_mcbond_it 0.379 r_chiral_restr 0.086 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6627 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling