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Crystal structure of the rat isoform of the succinate receptor SUCNR1 (GPR91) in complex with a nanobody
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XNV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 293.15 0.1M Na-Citrate
24-30% PEG400
0.05M NaSCN
2.5% 2,5-Hexanediol
1% DMSO
Crystal Properties Matthews coefficient Solvent content 3.07 59.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.22 α = 90 b = 164 β = 102.63 c = 63.42 γ = 90
Symmetry Space Group P 1 21 1
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 2017-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.999 SLS X06SA
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 1.42 41.55 88.2 0.763 2.92 17.88 198484 44.21
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 1.42 1.46 20.8 2.119 0.32 1.59
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 4XNV 2.12 41.55 41256 1950 61 0.18 0.178 0.216 0.2098 RANDOM 56.4
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] 11.4567 2.4984 -10.1644 -1.2923
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.6 t_omega_torsion 2.89 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 19.6 t_omega_torsion 2.89 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 6643 Nucleic Acid Atoms Solvent Atoms 299 Heterogen Atoms 374
Software Software Software Name Purpose BUSTER refinement XSCALE data scaling PHASER phasing PDB_EXTRACT data extraction XDS data reduction