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Crystal Structure of PDZ domain of sorting nexin 27 (SNX27) fused to the C-terminal residues (ESESKV) of GIRK3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OCS PDB ENTRY 2OCS
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 2.09 41.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.789 α = 90 b = 75.789 β = 90 c = 40.939 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ mirrors 2008-08-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007
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 1.68 50 86.3 0.039 39.53 4.8 8921 39.25
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) 1.68 1.71 45.2 0.174 6.68 3.3 232
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 (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 2OCS 1.68 37.9 8503 417 89.05 0.1609 0.15804 0.1561 0.22276 0.2208 RANDOM 21.419
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] 0.07 0.03 0.07 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.94 r_dihedral_angle_4_deg 23.174 r_dihedral_angle_3_deg 15.054 r_dihedral_angle_1_deg 5.91 r_scangle_it 5.898 r_scbond_it 3.466 r_mcangle_it 2.319 r_angle_refined_deg 1.976 r_mcbond_it 1.337 r_chiral_restr 0.127
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.94 r_dihedral_angle_4_deg 23.174 r_dihedral_angle_3_deg 15.054 r_dihedral_angle_1_deg 5.91 r_scangle_it 5.898 r_scbond_it 3.466 r_mcangle_it 2.319 r_angle_refined_deg 1.976 r_mcbond_it 1.337 r_chiral_restr 0.127 r_bond_refined_d 0.024 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 762 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling