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The Dvl2 PDZ Domain in Complex with the N2 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 VAPOR DIFFUSION, SITTING DROP 7.5 292 0.1 M HEPES, 0.8 M sodium phosphate, 0.8 M Potassium phosphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.23 44.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.675 α = 90 b = 43.554 β = 90 c = 54.86 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 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 1.00 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 1.38 50 99.3 0.046 32.1 5.5 21576
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) 1.38 1.43 94.6 0.397 2.8 4.3 2018
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 1.38 20 20391 1096 99.31 0.139 0.137 0.1359 0.166 0.1676 RANDOM 13.494
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] -0.66 -0.17 0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.528 r_dihedral_angle_4_deg 18.42 r_sphericity_free 16.502 r_dihedral_angle_3_deg 11.615 r_sphericity_bonded 8.475 r_scangle_it 7.228 r_dihedral_angle_1_deg 6.089 r_scbond_it 5.434 r_mcangle_it 5.38 r_mcbond_it 4.704
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.528 r_dihedral_angle_4_deg 18.42 r_sphericity_free 16.502 r_dihedral_angle_3_deg 11.615 r_sphericity_bonded 8.475 r_scangle_it 7.228 r_dihedral_angle_1_deg 6.089 r_scbond_it 5.434 r_mcangle_it 5.38 r_mcbond_it 4.704 r_rigid_bond_restr 3.205 r_mcbond_other 2.942 r_angle_refined_deg 1.6 r_angle_other_deg 0.936 r_nbd_refined 0.208 r_nbd_other 0.193 r_symmetry_vdw_refined 0.191 r_xyhbond_nbd_refined 0.189 r_symmetry_vdw_other 0.184 r_nbtor_refined 0.174 r_symmetry_hbond_refined 0.111 r_chiral_restr 0.103 r_nbtor_other 0.087 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 801 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 13
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction