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Crystal Structure of ZO-1 PDZ1 Bound to a Phage-Derived Ligand (WRRTTYL)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2H3M PDB Entry: 2H3M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 292 0.1 M Sodium Acetate, 0.2 M Ammonium Sulfate, 30% PEG 2000 Monomethyl Ether, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.72 54.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.425 α = 90 b = 52.425 β = 90 c = 92.932 γ = 90
Symmetry Space Group P 41 21 2
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 210 2004-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 1.00 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.61 50 99.6 0.052 31.9 7.3 17606
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.61 1.67 98.4 0.401 3.7 5.8 1690
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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: 2H3M 1.6 30 17664 17538 898 99.35 0.205 0.205 0.203 0.207 0.232 0.2332 RANDOM 27.636
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] -0.1 -0.1 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.276 r_dihedral_angle_4_deg 19.697 r_dihedral_angle_3_deg 11.458 r_dihedral_angle_1_deg 5.983 r_scangle_it 4.049 r_scbond_it 2.503 r_mcangle_it 1.642 r_angle_refined_deg 1.358 r_mcbond_it 1.181 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.276 r_dihedral_angle_4_deg 19.697 r_dihedral_angle_3_deg 11.458 r_dihedral_angle_1_deg 5.983 r_scangle_it 4.049 r_scbond_it 2.503 r_mcangle_it 1.642 r_angle_refined_deg 1.358 r_mcbond_it 1.181 r_nbtor_refined 0.302 r_symmetry_hbond_refined 0.273 r_symmetry_vdw_refined 0.215 r_nbd_refined 0.188 r_xyhbond_nbd_refined 0.112 r_chiral_restr 0.102 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 824 Nucleic Acid Atoms Solvent Atoms 109 Heterogen Atoms 4
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction