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Crystal structure of GPR52 ligand free form with rubredoxin 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 293 0.08-0.1 M magnesium sulphate, 0.1 M sodium cacodylate trihydrate pH 6.2, and 28-31% PEG300
Crystal Properties Matthews coefficient Solvent content 3.83 67.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.223 α = 90 b = 113.229 β = 90 c = 138.615 γ = 90
Symmetry Space Group I 2 2 2
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) 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 2.8 50 96.9 0.164 0.054 1 13.2 8.2 15032 47.78
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 2.8 2.9 96.1 0.967 0.328 0.895 1.7 8
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 2.8 29.25 11830 612 81.1 0.24217 0.24112 0.2446 0.26295 0.2631 RANDOM 61.372
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] 2.26 -3.97 1.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.237 r_long_range_B_refined 18.218 r_long_range_B_other 18.218 r_dihedral_angle_3_deg 16.099 r_dihedral_angle_4_deg 14.948 r_scangle_other 12.484 r_mcangle_other 11.827 r_mcangle_it 11.818 r_scbond_it 9.052 r_scbond_other 9.049
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.237 r_long_range_B_refined 18.218 r_long_range_B_other 18.218 r_dihedral_angle_3_deg 16.099 r_dihedral_angle_4_deg 14.948 r_scangle_other 12.484 r_mcangle_other 11.827 r_mcangle_it 11.818 r_scbond_it 9.052 r_scbond_other 9.049 r_mcbond_it 8.562 r_mcbond_other 8.537 r_dihedral_angle_1_deg 4.494 r_angle_refined_deg 1.44 r_angle_other_deg 0.805 r_chiral_restr 0.073 r_gen_planes_refined 0.042 r_gen_planes_other 0.036 r_bond_refined_d 0.008 r_bond_other_d 0.007 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 2761 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms 177
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing