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The crystal structure of the 2nd PDZ domain of the human NHERF-1 (SLC9A3R1)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 0.2M NaNO3, 0.1M BTProp, 20% PEG 3350, 10% Ethylene glycol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.88 57.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.304 α = 90 b = 54.715 β = 90 c = 96.724 γ = 90
Symmetry Space Group I 2 2 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 MARMOSAIC 225 mm CCD 2007-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.91830 SLS X10SA
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 1.5 39.53 95.8 0.066 0.066 18038 18038
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) 1.5 1.55 99.4 0.601 0.5 1826
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.5 39.53 17112 17112 902 95.75 0.17239 0.17239 0.1703 0.1793 0.21057 0.2187 RANDOM 20.533
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] -0.16 0.09 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.58 r_dihedral_angle_4_deg 13.226 r_dihedral_angle_3_deg 12.23 r_sphericity_free 9.037 r_scangle_it 6.091 r_dihedral_angle_1_deg 5.346 r_sphericity_bonded 4.534 r_scbond_it 4.1 r_mcangle_it 2.871 r_rigid_bond_restr 2.494
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.58 r_dihedral_angle_4_deg 13.226 r_dihedral_angle_3_deg 12.23 r_sphericity_free 9.037 r_scangle_it 6.091 r_dihedral_angle_1_deg 5.346 r_sphericity_bonded 4.534 r_scbond_it 4.1 r_mcangle_it 2.871 r_rigid_bond_restr 2.494 r_mcbond_it 2.086 r_angle_refined_deg 1.801 r_angle_other_deg 1.39 r_mcbond_other 0.912 r_symmetry_vdw_other 0.432 r_chiral_restr 0.262 r_nbd_refined 0.231 r_symmetry_hbond_refined 0.211 r_nbd_other 0.199 r_nbtor_refined 0.169 r_xyhbond_nbd_refined 0.156 r_symmetry_vdw_refined 0.133 r_nbtor_other 0.085 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d 0.002 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 700 Nucleic Acid Atoms Solvent Atoms 150 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing