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CRYSTAL STRUCTURE OF THE PTPN4 PDZ DOMAIN COMPLEXED WITH THE TAILORED PEPTIDE CYTO8-RETEV
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NFK PDB ENTRY 3NFK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 291 23% PEG 8000, 0.1 M MES PH 6.0, 0.2 M CALCIUM ACETATE, 0.143 MM AMMONIUM SULFATE
Crystal Properties Matthews coefficient Solvent content 3.37 63.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.71 α = 90 b = 80.88 β = 90 c = 170.23 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 291 PIXEL DECTRIS PILATUS 6M 2011-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 1.28268 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.09 46.8 94.2 0.049 0.056 0.025 14.2 4.7 30269 30269 2 54.44
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.09 2.2 63 0.51 0.022 1.7 3.1 1120
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT PDB ENTRY 3NFK 2.09 42.56 30234 1539 94.02 0.2297 0.2291 0.2327 0.2395 0.2448 RANDOM 65.36
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] 7.7697 3.324 -11.0937
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.29 t_omega_torsion 2.05 t_angle_deg 0.97 t_bond_d 0.007 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.29 t_omega_torsion 2.05 t_angle_deg 0.97 t_bond_d 0.007 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3066 Nucleic Acid Atoms Solvent Atoms 109 Heterogen Atoms 1
Software Software Software Name Purpose BUSTER-TNT refinement SCALA data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing