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Crystal structure of the 3rd PDZ domain of intestine- and kidney- enriched PDZ domain IKEPP (PDZD3)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G9O PDB ENTRY 1G9O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 2M (NH4)2SO4, 0.1M BIS-TRIS, PH=5.5
Crystal Properties Matthews coefficient Solvent content 2.1 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.15 α = 90 b = 97.95 β = 99.59 c = 59.5 γ = 90
Symmetry Space Group P 1 21 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 MARRESEARCH 2007-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA SLS X10SA
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 2 42.7 97.8 0.07 9.8 3.6 36079
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 2 2.1 94.7 0.28 3.7 3.1
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 PDB ENTRY 1G9O 2 50 34206 1798 97.9 0.196 0.193 0.1982 0.256 0.2571 RANDOM 16.85
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] -0.64 -0.59 0.19 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.09 r_dihedral_angle_4_deg 21.96 r_dihedral_angle_3_deg 14.858 r_scangle_it 9.687 r_scbond_it 7.078 r_dihedral_angle_1_deg 6.891 r_mcangle_it 4.324 r_mcbond_it 3.276 r_angle_refined_deg 1.475 r_angle_other_deg 0.923
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.09 r_dihedral_angle_4_deg 21.96 r_dihedral_angle_3_deg 14.858 r_scangle_it 9.687 r_scbond_it 7.078 r_dihedral_angle_1_deg 6.891 r_mcangle_it 4.324 r_mcbond_it 3.276 r_angle_refined_deg 1.475 r_angle_other_deg 0.923 r_symmetry_vdw_refined 0.259 r_symmetry_vdw_other 0.25 r_nbd_other 0.202 r_nbd_refined 0.2 r_xyhbond_nbd_refined 0.17 r_nbtor_refined 0.165 r_symmetry_hbond_refined 0.153 r_chiral_restr 0.088 r_nbtor_other 0.084 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4213 Nucleic Acid Atoms Solvent Atoms 388 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing