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Crystal structure of GPR52 ligand free form with flavodoxin fusion
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 0.1 M potassium acetate, 0.1 M sodium citrate pH 5.0, and 30% PEG400
Crystal Properties Matthews coefficient Solvent content 3.98 69.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.648 α = 90 b = 79.891 β = 90 c = 148.304 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 2019-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.000 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.9 50 97.6 0.235 0.991 11.8 9.2 18312
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3 2.748 0.4 0.98
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 2.9 28.43 16462 912 95.56 0.24548 0.24427 0.2445 0.26677 0.2655 RANDOM 78.363
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] 0.98 -0.66 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.657 r_long_range_B_refined 25.811 r_long_range_B_other 25.811 r_scangle_other 22.484 r_mcangle_it 20.066 r_mcangle_other 20.064 r_dihedral_angle_4_deg 19.31 r_scbond_it 17.212 r_scbond_other 17.207 r_dihedral_angle_3_deg 17.046
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.657 r_long_range_B_refined 25.811 r_long_range_B_other 25.811 r_scangle_other 22.484 r_mcangle_it 20.066 r_mcangle_other 20.064 r_dihedral_angle_4_deg 19.31 r_scbond_it 17.212 r_scbond_other 17.207 r_dihedral_angle_3_deg 17.046 r_mcbond_it 14.711 r_mcbond_other 14.708 r_dihedral_angle_1_deg 3.42 r_angle_refined_deg 1.541 r_angle_other_deg 0.81 r_chiral_restr 0.088 r_gen_planes_refined 0.041 r_gen_planes_other 0.034 r_bond_refined_d 0.008 r_bond_other_d 0.008 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 3339 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing