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Crystal Structure of the third PDZ domain of PSD-95
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BE9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 capillary contradiffusion 4.6 298 0.2M ammonium sulphate, 0.1M ammonium acetate trihydrate, 25%(w/v) PEG 4000, pH 4.6, capillary contradiffusion, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.95 36.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.322 α = 90 b = 42.152 β = 90 c = 47.602 γ = 92.08
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 CCD MAR CCD 165 mm 2008-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM16 0.97 ESRF BM16
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.35 47.619 92 0.062 0.062 16.074 2.4 73746 67847 13.018
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.4 92.9 0.411 0.411 1.84 2.3 6858
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 1BE9 1.35 47.619 73746 67844 3424 91.84 0.189 0.189 0.187 0.1884 0.216 0.2157 RANDOM 18.043
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] 0.15 0.09 -0.01 0.12 0.02 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.801 r_dihedral_angle_3_deg 13.723 r_dihedral_angle_4_deg 8.915 r_dihedral_angle_1_deg 6.488 r_scangle_it 5.728 r_scbond_it 3.97 r_mcangle_it 3.908 r_mcbond_it 2.704 r_angle_refined_deg 2.163 r_chiral_restr 0.134
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.801 r_dihedral_angle_3_deg 13.723 r_dihedral_angle_4_deg 8.915 r_dihedral_angle_1_deg 6.488 r_scangle_it 5.728 r_scbond_it 3.97 r_mcangle_it 3.908 r_mcbond_it 2.704 r_angle_refined_deg 2.163 r_chiral_restr 0.134 r_bond_refined_d 0.022 r_gen_planes_refined 0.016
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2964 Nucleic Acid Atoms Solvent Atoms 234 Heterogen Atoms 24
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection DENZO data reduction SCALEPACK data scaling