☰ Navigation Tabs
The crystal structure of the first PDZ domain of human NHERF-2 (SLC9A3R2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model SwissModel swissmodel generated model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 20% PEG 3350, 0.20M KSCN, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.93 36.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 26.556 α = 90 b = 39.867 β = 106.93 c = 37.278 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 MARMOSAIC 225 mm CCD 2006-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 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 35.66 100 0.0656 0.05 12.68 3.67 12062 12057
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 1.6 100 0.4595 0.322 5.4 3.64 2093
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 swissmodel generated model 1.5 35.66 12062 11448 609 99.96 0.15411 0.15411 0.15185 0.1619 0.19829 0.2006 RANDOM 14.108
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] -0.29 0.03 -0.63 0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.583 r_dihedral_angle_4_deg 17.97 r_dihedral_angle_3_deg 12.38 r_sphericity_free 9.877 r_dihedral_angle_1_deg 6.303 r_scangle_it 6.052 r_sphericity_bonded 5.218 r_scbond_it 4.131 r_mcangle_it 3.173 r_mcbond_it 2.188
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.583 r_dihedral_angle_4_deg 17.97 r_dihedral_angle_3_deg 12.38 r_sphericity_free 9.877 r_dihedral_angle_1_deg 6.303 r_scangle_it 6.052 r_sphericity_bonded 5.218 r_scbond_it 4.131 r_mcangle_it 3.173 r_mcbond_it 2.188 r_rigid_bond_restr 2.077 r_angle_refined_deg 1.941 r_angle_other_deg 1.222 r_mcbond_other 1.062 r_symmetry_vdw_refined 0.397 r_symmetry_vdw_other 0.382 r_chiral_restr 0.377 r_nbd_refined 0.276 r_nbd_other 0.235 r_xyhbond_nbd_refined 0.188 r_nbtor_refined 0.177 r_symmetry_hbond_refined 0.161 r_nbtor_other 0.092 r_bond_refined_d 0.021 r_gen_planes_refined 0.009 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 664 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling PHASER phasing