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Structure of the compact lumenal domain of yeast Ire1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Ire1 lumenal domain
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 1.6 M ammonium sulfate, 5% dioxane, 0.6% MeOH, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 4.01 69.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.3 α = 90 b = 103.3 β = 90 c = 401.4 γ = 120
Symmetry Space Group P 65 2 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 ADSC QUANTUM 4 tunable monochromoter 2005-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.116 ALS 8.3.1
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 2.983 48.4 90.8 0.106 11.8 3.9 24150 24150 -3 59.9
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 2.983 3.19 76.3 0.245 1.8 2.4 3260
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 (All) 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 FOURIER SYNTHESIS THROUGHOUT Ire1 lumenal domain 2.983 48.28 21745 21745 2380 82.1 0.24398 0.24398 0.24005 0.225 0.2794 0.265 RANDOM 41.442
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] 3.58 1.79 3.58 -5.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.768 r_dihedral_angle_3_deg 22.091 r_dihedral_angle_4_deg 19.186 r_dihedral_angle_1_deg 7.58 r_scangle_it 4.154 r_scbond_it 2.532 r_mcangle_it 2.508 r_angle_refined_deg 2.277 r_mcbond_it 1.376 r_nbtor_refined 0.353
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.768 r_dihedral_angle_3_deg 22.091 r_dihedral_angle_4_deg 19.186 r_dihedral_angle_1_deg 7.58 r_scangle_it 4.154 r_scbond_it 2.532 r_mcangle_it 2.508 r_angle_refined_deg 2.277 r_mcbond_it 1.376 r_nbtor_refined 0.353 r_symmetry_vdw_refined 0.335 r_nbd_refined 0.301 r_xyhbond_nbd_refined 0.221 r_chiral_restr 0.142 r_symmetry_hbond_refined 0.089 r_bond_refined_d 0.026 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 4858 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling CNS phasing