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Crystal structure of the PTPN4 PDZ domain complexed with the C-terminus of the GluN2A NMDA receptor subunit
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VPH PDB ENTRY 2VPH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 24% PEG 4000, 0.2M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.34 47.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.582 α = 90 b = 51.679 β = 90 c = 190.902 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 PSI PILATUS 6M 2009-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.9795 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.91 95.45 96.1 0.043 21.1 4.2 40560 38978 37.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.91 2.01 74.7 0.309 2 2.1 4287
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 2VPH 1.91 49.88 40490 38911 1959 95.84 0.218 0.2166 0.2245 0.2465 0.2393 RANDOM 54.07
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] 0.876 -6.5161 5.6401
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.12 t_omega_torsion 2.77 t_angle_deg 1.18 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2924 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms
Software Software Software Name Purpose XDS data scaling PHASER phasing BUSTER refinement XDS data reduction SCALA data scaling