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Crystal structure of an agonist bound GPCR
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ZTY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 293 100 mM HEPES sodium pH 7.0, 25% PEG 400, 220 mM Sodium sulfate decahydrate
Crystal Properties Matthews coefficient Solvent content 3.31 67.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.96 α = 90 b = 140.22 β = 90 c = 156.26 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 16M 2018-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1 SPring-8 BL41XU
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 fixed target
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 3.2 44.78 87.6 0.171 0.2 0.986 4.26 2.847 11476 96.93
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.28 90.4 0.673 0.789 0.627 1.22 2.796
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5zty 3.2 44.78 11475 531 87.7 0.231 0.23 0.262 0.3031 RANDOM 118.21
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] 20.7169 -22.8308 2.1138
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.89 t_omega_torsion 1.95 t_angle_deg 1.03 t_bond_d 0.009 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.89 t_omega_torsion 1.95 t_angle_deg 1.03 t_bond_d 0.009 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle 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 3471 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 29
Software Software Software Name Purpose BUSTER refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing