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The crystal structure of the second PDZ domain of human NHERF-2 (SLC9A3R2) interacting with a mode 1 PDZ binding motif
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1I92 1i92 and 1g9o experimental model PDB 1G9O 1i92 and 1g9o
Crystallization Crystal Properties Matthews coefficient Solvent content 1.89 34.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.803 α = 90 b = 37.677 β = 97.7 c = 40.34 γ = 90
Symmetry Space Group C 1 2 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 MARRESEARCH 2006-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.97646 SLS X10SA
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 1.45 39.97 98.5 0.0385 0.98 13265 13060
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.45 1.55 98 0.1403 6.45 0.98 2349
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 1i92 and 1g9o 1.45 39.97 13060 12418 641 98.46 0.13203 0.13203 0.12965 0.1287 0.18003 0.1811 RANDOM 14.015
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] 2.05 1.34 -1.13 -0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.109 r_dihedral_angle_4_deg 13.576 r_dihedral_angle_3_deg 10.62 r_sphericity_free 10.418 r_scangle_it 8.624 r_dihedral_angle_1_deg 6.535 r_scbond_it 6.273 r_sphericity_bonded 5.954 r_mcangle_it 4.686 r_mcbond_it 3.816
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.109 r_dihedral_angle_4_deg 13.576 r_dihedral_angle_3_deg 10.62 r_sphericity_free 10.418 r_scangle_it 8.624 r_dihedral_angle_1_deg 6.535 r_scbond_it 6.273 r_sphericity_bonded 5.954 r_mcangle_it 4.686 r_mcbond_it 3.816 r_rigid_bond_restr 2.851 r_mcbond_other 2.47 r_angle_refined_deg 1.594 r_angle_other_deg 0.957 r_symmetry_vdw_other 0.29 r_symmetry_vdw_refined 0.248 r_symmetry_hbond_refined 0.231 r_nbd_refined 0.217 r_nbd_other 0.197 r_xyhbond_nbd_refined 0.188 r_nbtor_refined 0.16 r_chiral_restr 0.094 r_nbtor_other 0.082 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 719 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement PHASER phasing