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Crystal structure of human orexin type 2 receptor in complex with vornorexant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7XRR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 7.5 293 0.15 mol/L Ammonium sulfate
0.1 mol/L HEPES pH7.5
10% v/v PEG 400
Crystal Properties Matthews coefficient Solvent content 3.17 61.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.46 α = 90 b = 90.88 β = 90 c = 111.54 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 EIGER X 9M 2025-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.0000 SPring-8 BL32XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.29 70.46 99.9 0.99 10.91 75.8 8106
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 3.29 3.49 0.552
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 7XRR 3.29 47.58 7657 412 99.95 0.24562 0.24287 0.2515 0.29529 0.3052 RANDOM 66.378
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] 5.16 -0.24 -4.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.786 r_long_range_B_refined 14.182 r_long_range_B_other 14.181 r_dihedral_angle_2_deg 10.052 r_scangle_other 8.827 r_mcangle_it 8.485 r_mcangle_other 8.484 r_scbond_it 5.603 r_scbond_other 5.595 r_dihedral_angle_1_deg 5.409
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.786 r_long_range_B_refined 14.182 r_long_range_B_other 14.181 r_dihedral_angle_2_deg 10.052 r_scangle_other 8.827 r_mcangle_it 8.485 r_mcangle_other 8.484 r_scbond_it 5.603 r_scbond_other 5.595 r_dihedral_angle_1_deg 5.409 r_mcbond_it 5.394 r_mcbond_other 5.393 r_angle_refined_deg 1.471 r_angle_other_deg 0.476 r_chiral_restr 0.063 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2520 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing