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Crystal Structure of the Second PDZ Domain of SAP97 in Complex with a GluR-A C-terminal Peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PDR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.2M SODIUM ACETATE, 0.1M TRIS-HCL, 30% PEG 4000 , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.97 37.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.76 α = 90 b = 54.44 β = 93.95 c = 55.14 γ = 90
Symmetry Space Group P 1 21 1
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 4 2004-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1
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 2.35 50 97.5 8429 8429
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.35 2.45 96.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1PDR 2.35 38.63 8005 422 100 0.22196 0.22196 0.21823 0.2154 0.29461 0.2911 RANDOM 45.075
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] 3.46 5.83 -1.86 -0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.595 r_dihedral_angle_3_deg 18.4 r_dihedral_angle_1_deg 7.116 r_scangle_it 3.56 r_scbond_it 2.188 r_angle_refined_deg 1.782 r_mcangle_it 1.651 r_mcbond_it 0.955 r_nbtor_refined 0.314 r_symmetry_vdw_refined 0.262
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.595 r_dihedral_angle_3_deg 18.4 r_dihedral_angle_1_deg 7.116 r_scangle_it 3.56 r_scbond_it 2.188 r_angle_refined_deg 1.782 r_mcangle_it 1.651 r_mcbond_it 0.955 r_nbtor_refined 0.314 r_symmetry_vdw_refined 0.262 r_nbd_refined 0.257 r_xyhbond_nbd_refined 0.155 r_chiral_restr 0.11 r_symmetry_hbond_refined 0.053 r_bond_refined_d 0.017 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1322 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ProDC data collection XDS data scaling MOLREP phasing