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Crystal structure of Scribble PDZ1 with human papillomavirus strain 16 E6 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6XA6 6XA6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293.15 2.5 M NaCl, 0.1 m Na HEPES pH 8.0
Crystal Properties Matthews coefficient Solvent content 5.17 76.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.611 α = 90 b = 70.611 β = 90 c = 140.782 γ = 120
Symmetry Space Group P 61 2 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 EIGER X 16M 2022-08-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95372 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.5 37.23 99.44 0.1008 0.999 23.29 6.2 7707 65.73
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.589 97.98 1.363 0.939 1.61
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 6XA6 2.5 37.23 1.35 7673 373 99.48 0.2747 0.2743 0.2772 0.2812 0.2882 72.32
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 23.7104 f_angle_d 1.6119 f_chiral_restr 0.0593 f_plane_restr 0.0173 f_bond_d 0.0151
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 737 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 65
Software Software Software Name Purpose PHENIX refinement DIALS data reduction Aimless data scaling PHASER phasing