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XFEL crystal structure of human melatonin receptor MT2 (N86D) in complex with 2-phenylmelatonin
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IRO PDB id:1IRO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 293 N-(2-Acetamido)iminodiacetic acid, PEG 400, ammonium acetate
Crystal Properties Matthews coefficient Solvent content 3.84 68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.7 α = 90 b = 145.8 β = 107.4 c = 77 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 293 PIXEL CS-PAD CXI-1 2017-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SLAC LCLS BEAMLINE CXI 1.30 SLAC LCLS CXI
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 injection
Measurement Diffraction ID Pulse Duration Pulse Repetition Rate Focal Spot Size Pulse Energy Photons Per Pulse 1 30 (fs) 120 9.83 (KeV)
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1 20704 22267 20704
Injection Diffraction ID Description Flow Rate Injector Diameter Injection Power Injector Nozzle Filter Size Carrier Solvent 1 0.357 (µl/min) undefined (µm) HPLC pump LCP LCP
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Split (All) 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 22 100 0.19 3.87 133 26228 76.61
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.23
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 id:1IRO 3.1 22 26179 1309 100 0.235 0.234 0.2848 0.262 0.3079 RANDOM 130.74
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] -53.7473 -31.5378 49.5135 4.2338
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 2.76 t_omega_torsion 1.81 t_angle_deg 0.96 t_bond_d 0.009 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 2.76 t_omega_torsion 1.81 t_angle_deg 0.96 t_bond_d 0.009 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 6045 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 47
Software Software Software Name Purpose BUSTER refinement CrystFEL data reduction CrystFEL data scaling PHASER phasing