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Structure of the PDZ4 domain from human PDZK1 (NHERF3) with the C-terminal residues (KSTQF) of human URAT1 transporter (SLC22A12)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EZI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1% 2-methyl-2,4-pentanediol,
2.5 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.63 53.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.915 α = 90 b = 44.915 β = 90 c = 174.671 γ = 120
Symmetry Space Group P 32 2 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 9M 2023-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.87313 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 1.43 40 93.2 0.143 0.023 0.996 14.7 40.1 30495
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 1.43 1.55 51.3 2.764 0.432 0.774 1.5 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 1.43 38.9 1.36 30481 1440 78.52 0.2093 0.2083 0.2093 0.2308 0.2316 31.76
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 12.9508 f_angle_d 0.5567 f_chiral_restr 0.0653 f_plane_restr 0.0047 f_bond_d 0.0031
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1347 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms
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