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Crystal structure of the human prostaglandin E receptor EP4 in complex with Fab and an antagonist Br-derivative
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5WV2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 293 24-31% PEG 300, 150 mM potassium sulfate, 100 mM MES (pH 5.5-6.5), 1% 1,2,3-heptanetriol, 0.2 mM ONO-AE3-208-Br, 2% DMSO
Crystal Properties Matthews coefficient Solvent content 4.44 72.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.97 α = 90 b = 392.23 β = 90 c = 81.08 γ = 90
Symmetry Space Group C 2 2 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 2016-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 0.9000 SPring-8 BL32XU
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 4.2 49.339 99.9 0.0716 0.741 0.982 4.31 15.076 22914 -3 65.9
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 4.2 4.45 99.9 0.676 6.993 0.3 0.59 15.356
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5WV2 4.2 49.339 1.33 22266 1117 97.16 0.3343 0.333 0.2974 0.3588 0.339 134.3258
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.102 f_angle_d 0.573 f_chiral_restr 0.041 f_plane_restr 0.005 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5577 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 30
Software Software Software Name Purpose XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction PHENIX phasing