☰ Navigation Tabs
The Dvl2 PDZ Domain in Complex with the N1 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 292 1.6 M tri-sodium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.4 48.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.303 α = 90 b = 52.187 β = 100.33 c = 31.911 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 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 1.5 50 98.3 0.065 19.3 5.1 34942
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) 1.5 1.55 96.8 0.636 2.6 4.9 3410
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 1.5 20 33035 1743 98.3 0.136 0.134 0.1368 0.182 0.1842 RANDOM 17.255
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] -0.49 0.61 0.32 0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.227 r_sphericity_free 14.781 r_dihedral_angle_3_deg 11.923 r_dihedral_angle_4_deg 10.478 r_scangle_it 7.804 r_sphericity_bonded 7.246 r_mcangle_it 6.34 r_scbond_it 5.941 r_dihedral_angle_1_deg 5.558 r_mcbond_it 5.219
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.227 r_sphericity_free 14.781 r_dihedral_angle_3_deg 11.923 r_dihedral_angle_4_deg 10.478 r_scangle_it 7.804 r_sphericity_bonded 7.246 r_mcangle_it 6.34 r_scbond_it 5.941 r_dihedral_angle_1_deg 5.558 r_mcbond_it 5.219 r_rigid_bond_restr 3.252 r_mcbond_other 2.601 r_angle_refined_deg 1.513 r_angle_other_deg 0.915 r_symmetry_vdw_other 0.252 r_nbd_refined 0.216 r_xyhbond_nbd_refined 0.199 r_nbd_other 0.195 r_nbtor_refined 0.181 r_symmetry_vdw_refined 0.136 r_symmetry_hbond_refined 0.11 r_chiral_restr 0.09 r_nbtor_other 0.086 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1559 Nucleic Acid Atoms Solvent Atoms 198 Heterogen Atoms 8
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction