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PDZK1 domain 4 in complex with C-terminal peptide of human PepT2.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4R2Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 292.15 0.1 M Trisodium citrate pH 6.45
20% PEG 4000
20 %(v/v) isopropanol
Crystal Properties Matthews coefficient Solvent content 2.98 58.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.4 α = 90 b = 54.4 β = 90 c = 150.76 γ = 120
Symmetry Space Group P 65 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 173 PIXEL DECTRIS PILATUS3 6M 2017-02-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 1.07166 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.5 47.12 99.7 0.06612 0.06711 33.85 35 21856 18.8597757139
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.59 99.3 0.963 0.9771 0.776 4.2 34.8
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4R2Z 1.50332103817 47.1117819659 1.36321607249 21854 1093 99.708002555 0.194841046699 0.193827423621 0.1937 0.214201883363 0.2157 5% 36.6794828473
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 14.9040965594 f_angle_d 0.835981574208 f_chiral_restr 0.0588887482759 f_bond_d 0.00700564800598 f_plane_restr 0.00504508991792
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 690 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms 6
Software Software Software Name Purpose Coot model building PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing