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Crystal structure of the complex between mouse PTP delta and neuroligin-3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YD6 2YD6, 4YFD, 4YFE, 3BIX experimental model PDB 4YFD 2YD6, 4YFD, 4YFE, 3BIX experimental model PDB 4YFE 2YD6, 4YFD, 4YFE, 3BIX experimental model PDB 3BIX 2YD6, 4YFD, 4YFE, 3BIX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 298 10% PEG 3350, 0.1 M ammonium iodide, 0.1 M MES-Na
Crystal Properties Matthews coefficient Solvent content 4.28 71.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.109 α = 90 b = 96.109 β = 90 c = 371.613 γ = 120
Symmetry Space Group P 32 1 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 PILATUS3 S 6M 2014-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 SPring-8 BL41XU
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 3.85 50 98.4 0.119 0.124 0.034 4.1 8.9 19070 142.02
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 4.22 4.3 98.5 0.339 0.373 0.148 0.582 5.1
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 THROUGHOUT 2YD6, 4YFD, 4YFE, 3BIX 3.85 49.69 1.35 19070 928 99.7 0.2547 0.2531 0.2533 0.2891 0.2905
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 14.42 f_angle_d 0.499 f_chiral_restr 0.046 f_plane_restr 0.004 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7273 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing