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Structure of the PDZ1 domain from human PDZK1 (NHERF3) with the C-terminal residues (VLKSTQF) of human URAT1 transporter (SLC22A12)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9RXN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 100 mM MES, pH 6.5,
700 mM NaCl,
18% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.2 43.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.887 α = 90 b = 35.887 β = 90 c = 72.069 γ = 120
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 9M 2025-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 1.00000 ESRF ID30B
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 1.69 31.1 93 0.156 0.024 0.999 16.7 42.2 9092
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 1.69 1.78 86.8 1.958 0.325 0.906 2.1 37
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.69 31.08 2 9091 398 78.33 0.188 0.187 0.1847 0.2105 0.2077 29.2
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.6743 f_angle_d 0.4655 f_chiral_restr 0.0385 f_plane_restr 0.005 f_bond_d 0.0021
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 859 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement autoPROC data processing MxCuBE data collection PHASER phasing Coot model building MolProbity model building XDS data reduction STARANISO data scaling