☰ Navigation Tabs
Crystal structure of SNX5-PX domain in P21 space group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HPB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 277 The protein solution in the final superdex-75 buffer (20 mM Tris.HCl, 100 mM NaCl, 0.02% NaN3, pH 8.0) was concentrated to 8 mg/ml and crystallization were obtained using an optimized crystallization condition of 8ul of protein vs 1ul of reservoir solution (0.2M NH4CH3COO, 0.1M Sodium cacodylate tryhydrate pH 6.5, 30% PEG 4000), VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.300956 46.543972
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.598 α = 90 b = 41.424 β = 92.98 c = 47.227 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 RIGAKU SATURN 944 MIRRORS 2007-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT
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 1.47 31.12 98.3 0.043 20.1 4.13 28322 3
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) 1.47 1.52 90.8 0.325 1.4 2.65
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 3HPB 1.47 31.12 26873 1440 98.2 0.187 0.184 0.1805 0.234 0.2308 RANDOM 26.45
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] -0.1 -0.01 0.61 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.13 r_sphericity_free 14.952 r_dihedral_angle_4_deg 14.311 r_dihedral_angle_3_deg 12.856 r_sphericity_bonded 11.584 r_scangle_it 8.036 r_dihedral_angle_1_deg 5.739 r_scbond_it 5.567 r_mcangle_it 4.047 r_rigid_bond_restr 3.334
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.13 r_sphericity_free 14.952 r_dihedral_angle_4_deg 14.311 r_dihedral_angle_3_deg 12.856 r_sphericity_bonded 11.584 r_scangle_it 8.036 r_dihedral_angle_1_deg 5.739 r_scbond_it 5.567 r_mcangle_it 4.047 r_rigid_bond_restr 3.334 r_mcbond_it 2.827 r_angle_refined_deg 1.296 r_chiral_restr 0.097 r_gen_planes_refined 0.015 r_bond_refined_d 0.013 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1323 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms 1
Software Software Software Name Purpose StructureStudio data collection PHASER phasing REFMAC refinement d*TREK data reduction d*TREK data scaling