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Crystal Structure of Human Lysophosphatidic Acid Receptor 1 in complex with ONO9780307
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3V2Y PDB ids 3V2Y and 4EIY experimental model PDB 4EIY PDB ids 3V2Y and 4EIY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 5.5 293 0.1 M sodium citrate (pH 5.5),
34 - 38% (v/v) PEG400 and
200 mM ammonium acetate
Crystal Properties Matthews coefficient Solvent content 2.9 57.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.28 α = 90 b = 112.15 β = 90 c = 154.63 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 CCD MARMOSAIC 300 mm CCD 2012-06-05 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2012-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.033 APS 23-ID-D 2 SYNCHROTRON APS BEAMLINE 23-ID-B 1.033 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 45 85 0.19 4.7 4 10576 37.83
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.16 75 0.46 1.4 2.1
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 ids 3V2Y and 4EIY 3 30 10576 531 83.6 0.2556 0.2543 0.3254 0.2805 0.3581 RANDOM 78.03
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] -3.0953 -1.5013 4.5966
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 2.95 t_omega_torsion 2.08 t_angle_deg 1.08 t_bond_d 0.01 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 2.95 t_omega_torsion 2.08 t_angle_deg 1.08 t_bond_d 0.01 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 2991 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 56
Software Software Software Name Purpose BUSTER refinement XDS data reduction SCALA data scaling PHASER phasing