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Crystal structure of PDZ3 domain of PSD-95 protein complexed with a peptide ligand KKETWV
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BE9 pdb entry 1BE9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.9 288 1.0 M sodium citrate, 0.1 M HEPES, 10 mM sodium chloride, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 2.4 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.978 α = 90 b = 89.978 β = 90 c = 89.978 γ = 90
Symmetry Space Group P 41 3 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 MARRESEARCH 2003-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 1.0 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.54 30 96.2 18320 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.54 1.63 95.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 1BE9 1.54 19.65 1 17356 17356 953 96.4 0.1929 0.19099 0.2058 0.22926 RANDOM 16.235
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.823 r_scangle_it 4.694 r_scbond_it 2.842 r_mcangle_it 1.962 r_angle_refined_deg 1.558 r_mcbond_it 1.072 r_angle_other_deg 0.907 r_symmetry_vdw_other 0.383 r_symmetry_vdw_refined 0.339 r_nbd_other 0.268
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.823 r_scangle_it 4.694 r_scbond_it 2.842 r_mcangle_it 1.962 r_angle_refined_deg 1.558 r_mcbond_it 1.072 r_angle_other_deg 0.907 r_symmetry_vdw_other 0.383 r_symmetry_vdw_refined 0.339 r_nbd_other 0.268 r_symmetry_hbond_refined 0.251 r_nbd_refined 0.24 r_xyhbond_nbd_refined 0.205 r_chiral_restr 0.088 r_nbtor_other 0.085 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_gen_planes_other 0.004 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 919 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling XTALVIEW refinement