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Crystal structure of the Orexin-1 receptor in complex with suvorexant at 2.29 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DJH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.2 284 0.1M TRISODIUM CITRATE
50mM SODIUM CHLORIDE
50mM LITHIUM SULPHATE
15-34% PEG400
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.9 α = 90 b = 158.47 β = 95.31 c = 183.62 γ = 90
Symmetry Space Group I 1 2 1
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 PILATUS3 S 6M 2012-09-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.97949 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 2.29 44.39 92.9 0.14 0.985 4.8 5.4 45066
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.29 2.48 52.4 0.397
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 4DJH 2.26 44.38 45066 2243 58.8 0.187 0.186 0.2246 0.211 0.2507 RANDOM 46.25
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] -3.6696 2.5557 -1.5257 5.1952
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.27 t_omega_torsion 2.81 t_angle_deg 1.03 t_bond_d 0.01 t_dihedral_angle_d t_gen_planes t_it t_nbd t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4828 Nucleic Acid Atoms Solvent Atoms 148 Heterogen Atoms 785
Software Software Software Name Purpose BUSTER refinement XDS data reduction STARANISO data scaling PHASER phasing