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Crystal Structure of PDZ domain of sorting nexin 27 (SNX27) fused to the Gly-Gly linker followed by C-terminal (ESESKV) of GIRK3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QE1 PDB ENTRY 3QE1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 0.2 M calcium chloride, 0.1 M HEPES, 28% v/v PEG400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.11 41.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.795 α = 90 b = 59.795 β = 90 c = 53.606 γ = 90
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 325 mm CCD mirrors 2009-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 SSRL BL9-2
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 1.88 42.28 99.79 0.045 37.3 7.2 7380 7380 14.216
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) 1.88 1.91 100 0.106 19.4 7.2 384
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 (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 3QE1 1.88 42.28 7380 7380 354 99.79 0.14688 0.14427 0.1428 0.20305 0.2026 RANDOM 19.074
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] -0.68 -0.68 1.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.063 r_dihedral_angle_3_deg 15.269 r_dihedral_angle_4_deg 9.101 r_dihedral_angle_1_deg 6.354 r_scangle_it 5.72 r_scbond_it 3.392 r_mcangle_it 2.432 r_angle_refined_deg 2.02 r_mcbond_it 1.405 r_chiral_restr 0.223
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.063 r_dihedral_angle_3_deg 15.269 r_dihedral_angle_4_deg 9.101 r_dihedral_angle_1_deg 6.354 r_scangle_it 5.72 r_scbond_it 3.392 r_mcangle_it 2.432 r_angle_refined_deg 2.02 r_mcbond_it 1.405 r_chiral_restr 0.223 r_bond_refined_d 0.023 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 798 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling