☰ Navigation Tabs
The Dvl2 PDZ Domain in Complex with the N3 Inhibitory Peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CBX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 292 1.0 M Ammonium citrate tribasic, 0.1 M BIS-TRIS propane, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 1.99 38.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.617 α = 90 b = 52.617 β = 90 c = 171.098 γ = 120
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 315 2006-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 ALS 5.0.2
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 1.75 50 99.5 0.058 19.8 3.8 26928
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 1.75 1.81 99.4 0.436 3.5 3.7
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 3CBX 1.75 20 25423 1348 99.6 0.19 0.188 0.1939 0.238 0.2434 RANDOM 23.02
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] -0.43 -0.22 -0.43 0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.951 r_dihedral_angle_4_deg 14.912 r_dihedral_angle_3_deg 13.04 r_dihedral_angle_1_deg 6.602 r_scangle_it 5.302 r_mcangle_it 4.174 r_scbond_it 3.966 r_mcbond_it 3.59 r_angle_refined_deg 1.458 r_angle_other_deg 0.878
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.951 r_dihedral_angle_4_deg 14.912 r_dihedral_angle_3_deg 13.04 r_dihedral_angle_1_deg 6.602 r_scangle_it 5.302 r_mcangle_it 4.174 r_scbond_it 3.966 r_mcbond_it 3.59 r_angle_refined_deg 1.458 r_angle_other_deg 0.878 r_mcbond_other 0.73 r_symmetry_vdw_other 0.242 r_symmetry_vdw_refined 0.21 r_nbd_refined 0.192 r_nbd_other 0.191 r_nbtor_refined 0.173 r_xyhbond_nbd_refined 0.161 r_symmetry_hbond_refined 0.134 r_chiral_restr 0.086 r_nbtor_other 0.083 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2299 Nucleic Acid Atoms Solvent Atoms 157 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction