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Crystal structure of GPR52 in complex with agonist c17
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Rosetta modelling
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 5 293 0.13-0.18 M sodium acetate,
0.1 M sodium citrate PH5.0,
32-35% PEG400
Crystal Properties Matthews coefficient Solvent content 4.19 70.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.97 α = 90 b = 88.36 β = 90 c = 156.28 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 PIXEL DECTRIS EIGER X 16M 2018-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim 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 2.2 50 99 0.177 0.034 0.443 18.3 26.5 42939
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.28 99.3 2.885 0.034 0.443 0.98 17.5
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 Rosetta modelling 2.2 41.89 40732 2108 99.37 0.19499 0.1937 0.1992 0.21982 0.2228 RANDOM 75.278
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] -3.04 3.74 -0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.882 r_long_range_B_other 20.259 r_long_range_B_refined 20.258 r_dihedral_angle_4_deg 19.804 r_scangle_other 17.398 r_scbond_it 16.663 r_scbond_other 16.659 r_dihedral_angle_3_deg 14.087 r_mcangle_it 12.283 r_mcangle_other 12.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.882 r_long_range_B_other 20.259 r_long_range_B_refined 20.258 r_dihedral_angle_4_deg 19.804 r_scangle_other 17.398 r_scbond_it 16.663 r_scbond_other 16.659 r_dihedral_angle_3_deg 14.087 r_mcangle_it 12.283 r_mcangle_other 12.28 r_mcbond_it 11.647 r_mcbond_other 11.618 r_dihedral_angle_1_deg 5.437 r_angle_refined_deg 1.662 r_angle_other_deg 0.478 r_chiral_restr 0.075 r_gen_planes_refined 0.054 r_gen_planes_other 0.046 r_bond_refined_d 0.011 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3469 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms 401
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing