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PDZ3 domain of PSD-95 protein complexed with KKETPV peptide ligand
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 6.9 295 1.0 M sodium citrate, 0.1 M HEPES, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.4 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.663 α = 90 b = 89.663 β = 90 c = 89.663 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 2004-03-27 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 1.99 23.96 99.7 6 11.58 8916 8916 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 1.99 2.06 99.1
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 (All) 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 1.99 19.57 1 8486 8486 423 99.72 0.2328 0.22788 0.2247 0.2342 0.2961 RANDOM 25.567
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 9.029 r_scangle_it 6.682 r_scbond_it 4.129 r_angle_refined_deg 2.721 r_mcangle_it 2.599 r_mcbond_it 1.618 r_angle_other_deg 1.223 r_symmetry_vdw_refined 0.398 r_symmetry_vdw_other 0.358 r_nbd_other 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 9.029 r_scangle_it 6.682 r_scbond_it 4.129 r_angle_refined_deg 2.721 r_mcangle_it 2.599 r_mcbond_it 1.618 r_angle_other_deg 1.223 r_symmetry_vdw_refined 0.398 r_symmetry_vdw_other 0.358 r_nbd_other 0.28 r_symmetry_hbond_refined 0.251 r_nbd_refined 0.239 r_xyhbond_nbd_refined 0.18 r_chiral_restr 0.175 r_nbtor_other 0.107 r_bond_refined_d 0.038 r_gen_planes_refined 0.013 r_gen_planes_other 0.008 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 908 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction d*TREK data scaling XTALVIEW refinement