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Structural Insights into the Extracellular Recognition of the Human Serotonin 2B Receptor by an Antibody
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NC3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 7.7 293 Tris/HCL pH 7.7, 60 mM Sodium/Potassium Tartrate, 25% PEG400.
Crystal Properties Matthews coefficient Solvent content 3.07 64.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.29 α = 90 b = 118.86 β = 90.37 c = 145.38 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 2014-01-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SLAC LCLS BEAMLINE CXI 1.56 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 35 (fs) 120 7.95 (KeV) 390000000000
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1 52291 52291
Injection Diffraction ID Description Flow Rate Injector Diameter Injection Power Injector Nozzle Filter Size Carrier Solvent 1 undefined (µl/min) undefined (µm)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 35.64 100 4.3 310.3 48606 90.32
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 3.1 100 0.34 0.4 120.26
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 4NC3 3 35.64 48606 2259 99.9 0.228 0.227 0.2465 0.247 0.2666 RANDOM 106.1
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] 7.2629 2.1576 -22.6624 15.3994
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 4.08 t_other_torsion 2.31 t_angle_deg 0.76 t_bond_d 0.005 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 4.08 t_other_torsion 2.31 t_angle_deg 0.76 t_bond_d 0.005 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 12298 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 86
Software Software Software Name Purpose BUSTER refinement CrystFEL data reduction PHASER phasing CrystFEL data scaling