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Structure of the PDZ4 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 9RXP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 100 mM Tris pH 8.5, 100mM NaCl, 18% PEG 10000, 20% Glycerol
Crystal Properties Matthews coefficient Solvent content 3.39 63.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.404 α = 90 b = 52.404 β = 90 c = 195.771 γ = 90
Symmetry Space Group P 43 21 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 PILATUS 6M 2024-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM07 0.979507 ESRF BM07
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 49 90.2 0.15 0.021 1 20.8 48.9 12585 32.42
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 2.13 86.4 2.32 0.52 0.878 2.7 41.7
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 2 24.32 1.34 12547 653 64.88 0.2002 0.1979 0.1963 0.2416 0.2379 42.23
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 12.5526 f_angle_d 0.7445 f_chiral_restr 0.0515 f_bond_d 0.0104 f_plane_restr 0.0052
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1390 Nucleic Acid Atoms Solvent Atoms 115 Heterogen Atoms 6
Software Software Software Name Purpose PHENIX refinement MxCuBE data collection autoPROC data processing STARANISO data scaling PHASER phasing Coot model building MolProbity model building XDS data reduction