☰ Navigation Tabs
XFEL MT1R structure by ligand exchange from agomelatine to 2-phenylmelatonin.
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ME5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 293 60-100 mM potassium phosphate monobasic, 100 mM HEPES pH 7.0, 32-35% PEG 400, 1 mM of target ligand 2-phenylmelatonin, 2.5% DMSO, 1.5% propan-2-ol.
Crystal Properties Matthews coefficient Solvent content 4.04 69.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.2 α = 90 b = 122.2 β = 90 c = 122.6 γ = 90
Symmetry Space Group P 4 21 2
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 2018-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SLAC LCLS BEAMLINE CXI 1.33 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 1.5 9.5 (KeV)
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1 65260 87453 65260
Injection Diffraction ID Description Flow Rate Injector Diameter Injection Power Injector Nozzle Filter Size Carrier Solvent 1 0.2 (µl/min) undefined (µm)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 3.3 30 100 0.998 0.119 8.5 1663 14561
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.3 3.39 0.163 3.44
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 6me5 3.3 30 13778 728 99.75 0.2609 0.2585 0.3075 0.2661 RANDOM 114.238
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] -2.39 -2.39 4.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.6 r_dihedral_angle_3_deg 14.772 r_dihedral_angle_4_deg 12.841 r_dihedral_angle_1_deg 5.832 r_angle_refined_deg 1.109 r_angle_other_deg 0.907 r_chiral_restr 0.059 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.6 r_dihedral_angle_3_deg 14.772 r_dihedral_angle_4_deg 12.841 r_dihedral_angle_1_deg 5.832 r_angle_refined_deg 1.109 r_angle_other_deg 0.907 r_chiral_restr 0.059 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3648 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement PHASER phasing PDB_EXTRACT data extraction CrystFEL data reduction CrystFEL data scaling