☰ Navigation Tabs
Crystal structure of the 3rd PDZ domain of human discs large homologue 2, DLG2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TP5 Swissmodel based upon the coordinates of pdb entries 1TP5, 1TP3, 1BFE and 1BE9. experimental model PDB 1TP3 Swissmodel based upon the coordinates of pdb entries 1TP5, 1TP3, 1BFE and 1BE9. experimental model PDB 1BFE Swissmodel based upon the coordinates of pdb entries 1TP5, 1TP3, 1BFE and 1BE9. experimental model PDB 1BE9 Swissmodel based upon the coordinates of pdb entries 1TP5, 1TP3, 1BFE and 1BE9.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 25.5% PEG 3350; 0.17M (NH4)2SO4; 15% glycerol , VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.23 44.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.155 α = 90 b = 56.07 β = 90 c = 60.472 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 CCD MARMOSAIC 225 mm CCD 2006-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.97646 SLS X10SA
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 1.5 50 98.8 30918
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.5 1.55 97.5
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 (All) 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 Swissmodel based upon the coordinates of pdb entries 1TP5, 1TP3, 1BFE and 1BE9. 1.5 41.13 29281 29281 1559 98.79 0.12987 0.12987 0.12686 0.1254 0.18688 0.1852 RANDOM 9.045
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] -0.32 -0.03 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.522 r_dihedral_angle_4_deg 15.536 r_dihedral_angle_3_deg 11.168 r_sphericity_free 9.239 r_scangle_it 7.254 r_dihedral_angle_1_deg 5.921 r_scbond_it 5.844 r_sphericity_bonded 4.868 r_mcangle_it 4.512 r_mcbond_it 4.032
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.522 r_dihedral_angle_4_deg 15.536 r_dihedral_angle_3_deg 11.168 r_sphericity_free 9.239 r_scangle_it 7.254 r_dihedral_angle_1_deg 5.921 r_scbond_it 5.844 r_sphericity_bonded 4.868 r_mcangle_it 4.512 r_mcbond_it 4.032 r_rigid_bond_restr 2.738 r_mcbond_other 2.556 r_angle_refined_deg 1.324 r_angle_other_deg 0.858 r_symmetry_vdw_other 0.377 r_symmetry_vdw_refined 0.264 r_nbd_refined 0.202 r_symmetry_hbond_refined 0.198 r_nbd_other 0.192 r_xyhbond_nbd_refined 0.182 r_nbtor_refined 0.169 r_nbtor_other 0.083 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1546 Nucleic Acid Atoms Solvent Atoms 367 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PHASER phasing