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Crystal structure of human IRE1 cytoplasmic kinase-RNase region - complex with imidazopyridine compound 3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Z7G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 Apo-hIRE1 was crystallized by hanging-drop vapor diffusion by mixing IRE1 (at 2 mg/mL) with reservoir solution containing 18-20% PEG3350, 0.2 M sodium malonate and 0.1 Bis-Trispropane (pH 6.5) in a 1:1 ratio. Crystals were briefly (30 sec) soaked in 22% PEG3350, 0.2 M Na Malonate, 0.1 M Bis-Trispropane (pH 7.5) and 25% ethylene glycol before plunging into liquid N2.
Crystal Properties Matthews coefficient Solvent content 2.83 56.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.678 α = 90 b = 81.957 β = 90 c = 168.682 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 2M 2013-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92 Diamond I04-1
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 2.9 46.36 99.7 0.201 7.5 6.6 24770 79.38
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) 2.9 3.08 99 1.44 1.4 6.4
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 4Z7G 2.9 46.36 24770 1260 99.55 0.2015 0.2002 0.2283 0.2248 0.257 RANDOM 86.73
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] 17.1244 -1.469 -15.6554
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 21.08 t_omega_torsion 2.43 t_angle_deg 1.14 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 21.08 t_omega_torsion 2.43 t_angle_deg 1.14 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6186 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms 5
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling