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Structure of the PDZ1 domain from human NHERF1 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 4MPA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.4 293 100 mM sodium acetate pH 4.8
200 mM ammonium acetate
24% PEG 4000
Crystal Properties Matthews coefficient Solvent content 1.99 38.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.923 α = 90 b = 51.469 β = 90 c = 63.266 γ = 90
Symmetry Space Group P 21 21 21
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 4M 2022-09-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.96770 ESRF MASSIF-3
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 1.38 40 99.3 0.091 0.01 0.999 50.1 86.8 32381 13.28
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 1.38 1.41 92.1 0.461 0.085 0.983 9.1 56.3
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 1.38 38.2 1.43 32372 1659 99.28 0.1616 0.1604 0.1607 0.1826 0.1835 19.73
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 13.561 f_angle_d 1.0404 f_chiral_restr 0.0829 f_bond_d 0.0104 f_plane_restr 0.0099
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1380 Nucleic Acid Atoms Solvent Atoms 244 Heterogen Atoms 4
Software Software Software Name Purpose PHENIX refinement MxCuBE data collection autoPROC data processing MolProbity model building Coot model building XDS data reduction