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Crystal structure of the second PDZ domain from human Zona Occludens-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FNE PDB ENTRY 2FNE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.3 283 12% PEG8000, 0.1M Tris-HCl, pH8.3, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Crystal Properties Matthews coefficient Solvent content 2.23 44.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.177 α = 80.05 b = 41.325 β = 68.63 c = 41.292 γ = 68.52
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate 2006-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.75 20 15928
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 2FNE 1.75 20 15928 804 91.47 0.208 0.206 0.2029 0.237 0.2362 RANDOM 27.367
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] 0.42 -0.72 -0.17 -0.06 1.2 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.479 r_dihedral_angle_4_deg 18.205 r_dihedral_angle_3_deg 12.369 r_dihedral_angle_1_deg 6.317 r_scangle_it 4.213 r_scbond_it 2.511 r_mcangle_it 1.544 r_angle_refined_deg 1.498 r_mcbond_it 0.854 r_chiral_restr 0.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.479 r_dihedral_angle_4_deg 18.205 r_dihedral_angle_3_deg 12.369 r_dihedral_angle_1_deg 6.317 r_scangle_it 4.213 r_scbond_it 2.511 r_mcangle_it 1.544 r_angle_refined_deg 1.498 r_mcbond_it 0.854 r_chiral_restr 0.093 r_bond_refined_d 0.014 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1224 Nucleic Acid Atoms Solvent Atoms 203 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection AUTOMAR data reduction