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Crystal Structure of the third PDZ domain of PSD-95 protein E401R mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3K82
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 298 0.2 M ammonium sulphate, 25% w/v PEG 4000, 0.1 M sodium acetate
Crystal Properties Matthews coefficient Solvent content 1.7 27.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.905 α = 90 b = 36.707 β = 90 c = 62.833 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 PILATUS 6M 2025-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97934 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 0.95 19.32 93.1 0.027 0.031 0.015 0.999 19.7 3.9 45187 11.36
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.95 0.97 46.2 0.896 1.164 0.735 0.437 2
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 0.95 19.32 1.18 45131 2351 92.63 0.1421 0.1407 0.1392 0.1679 0.164 16.96
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 11.4885 f_angle_d 1.2786 f_chiral_restr 0.1046 f_plane_restr 0.0229 f_bond_d 0.0152
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 779 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 8
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction