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Crystal Structure Analysis of the PDZ Domain Derived from the Tight Junction Regulating Protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VWR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 23% PEG 8000, 0.2M sodium acetate, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.15 42.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.493 α = 90 b = 51.21 β = 120 c = 33.291 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 210r 2011-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
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 1.199 30 99.1 0.062 13.1 27352 27350 -3 10.91
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 1.2 1.22 98.4 0.184 5.1 7.2 1332
Refinement Statistics Diffraction ID Structure Solution 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 2vwr 1.199 26.195 27352 27350 1396 99 0.1457 0.1447 0.1394 0.1639 0.1581 RANDOM 15.669
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] -0.0773 0.4067 -0.5969 0.6742
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.444 f_angle_d 1.087 f_chiral_restr 0.075 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 670 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing PHENIX refinement HKL-2000 data reduction SCALEPACK data scaling