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The Dvl2 PDZ Domain in Complex with the C1 Inhibitory Peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1L6O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.8 292 60% 2-Methyl-2,4-pentanediol, 0.1 M sodium acetate, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.25 45.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.214 α = 90 b = 61.112 β = 90 c = 65.818 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 2006-02-15 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 1.7 50 99.6 0.069 16.9 4.6 23342
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 1.7 1.76 99.9 0.463 3.2 4.5
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 1L6O 1.7 20 22027 1158 99.5 0.187 0.185 0.1919 0.227 0.2343 RANDOM 27.92
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] -1.83 1.54 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.185 r_dihedral_angle_4_deg 17.276 r_dihedral_angle_3_deg 11.496 r_dihedral_angle_1_deg 5.922 r_scangle_it 4.857 r_mcangle_it 4.1 r_scbond_it 3.763 r_mcbond_it 3.583 r_angle_refined_deg 1.536 r_angle_other_deg 0.899
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.185 r_dihedral_angle_4_deg 17.276 r_dihedral_angle_3_deg 11.496 r_dihedral_angle_1_deg 5.922 r_scangle_it 4.857 r_mcangle_it 4.1 r_scbond_it 3.763 r_mcbond_it 3.583 r_angle_refined_deg 1.536 r_angle_other_deg 0.899 r_mcbond_other 0.795 r_symmetry_vdw_other 0.24 r_symmetry_vdw_refined 0.228 r_nbd_refined 0.197 r_nbd_other 0.188 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.167 r_symmetry_hbond_refined 0.139 r_chiral_restr 0.099 r_nbtor_other 0.083 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 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 1558 Nucleic Acid Atoms Solvent Atoms 121 Heterogen Atoms 17
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction