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Crystal Structure of a nanobody-stabilized active state of the kappa-opioid receptor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DJH PDB 4DJH, 5C1M, 1M6T experimental model PDB 5C1M PDB 4DJH, 5C1M, 1M6T experimental model PDB 1M6T PDB 4DJH, 5C1M, 1M6T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 293 100 mM Bis-tris pH 6.5-7.0, 140-200 mM magnesium sulfate hydrate, 100 mM sodium citrate tribasic dehydrate, 10 mM Manganese(II) chloride tetrahydrate, 28-30% PEG400
Crystal Properties Matthews coefficient Solvent content 3.66 66.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.31 α = 90 b = 150.75 β = 105.66 c = 100.28 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 123 PIXEL DECTRIS EIGER X 16M 2016-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0330 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 3.1 46.94 93.6 0.187 0.988 4 3 30278 78.82
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.27 88.2 0.961 0.537 0.9 2.5
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 PDB 4DJH, 5C1M, 1M6T 3.1 46.94 30255 1505 93.5 0.255 0.254 0.2708 0.275 0.2915 RANDOM 85.74
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] -29.6548 -3.2357 21.5032 8.1516
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 2.54 t_other_torsion 1.57 t_angle_deg 0.95 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_omega_torsion 2.54 t_other_torsion 1.57 t_angle_deg 0.95 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 6006 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 136
Software Software Software Name Purpose BUSTER refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing