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Crystal structure of the third PDZ domain of SAP-102 in complex with a fluorogenic peptide-based ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3JVQ PDB entry 3JVQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 1.0 M Sodium citrate, 0.1 M Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.41 48.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.597 α = 90 b = 54.215 β = 90 c = 86.023 γ = 90
Symmetry Space Group P 21 21 21
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 270 Toroidal focusing mirror 2009-02-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A 0.97000 NSLS X6A
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 1.5 50 99.8 0.061 28.19 7.2 37896 37820 -3 16.346
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 1.5 1.55 100 0.24 0.24 6.94 7.1 3720
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 3JVQ 1.5 45.87 35937 35869 1886 99.81 0.18659 0.18659 0.18511 0.1826 0.21442 0.2128 RANDOM 18.124
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] 0.55 0.56 -1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.841 r_dihedral_angle_4_deg 23.569 r_dihedral_angle_3_deg 15.012 r_dihedral_angle_1_deg 7.415 r_scangle_it 6.795 r_scbond_it 4.644 r_mcangle_it 3.408 r_mcbond_it 2.193 r_angle_refined_deg 1.289 r_symmetry_vdw_refined 0.344
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.841 r_dihedral_angle_4_deg 23.569 r_dihedral_angle_3_deg 15.012 r_dihedral_angle_1_deg 7.415 r_scangle_it 6.795 r_scbond_it 4.644 r_mcangle_it 3.408 r_mcbond_it 2.193 r_angle_refined_deg 1.289 r_symmetry_vdw_refined 0.344 r_nbtor_refined 0.326 r_nbd_refined 0.316 r_symmetry_hbond_refined 0.216 r_xyhbond_nbd_refined 0.162 r_chiral_restr 0.06 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1549 Nucleic Acid Atoms Solvent Atoms 340 Heterogen Atoms 4
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling