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Crystal structure of mouse SNX25 PX domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XDZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1.8 M Magnesium sulfate hydrate, 0.1 M Sodium acetate trihydrate pH 4.8
Crystal Properties Matthews coefficient Solvent content 3.75 67.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.68 α = 90 b = 92.68 β = 90 c = 449.521 γ = 120
Symmetry Space Group P 61 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 PIXEL DECTRIS PILATUS3 6M 2017-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.978 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.4 39.97 99.9 0.078 0.084 0.029 0.995 16.6 7.8 46187
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.48 99.9 0.78 0.832 0.285 0.804 8.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.4 39 43809 2319 99.83 0.20074 0.19858 0.2022 0.24186 0.2443 RANDOM 54.811
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] 0.02 0.01 0.02 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.732 r_dihedral_angle_4_deg 24.131 r_dihedral_angle_3_deg 18.265 r_long_range_B_refined 13.653 r_long_range_B_other 13.652 r_scangle_other 10.934 r_mcangle_it 9.768 r_mcangle_other 9.767 r_scbond_it 7.96 r_scbond_other 7.959
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.732 r_dihedral_angle_4_deg 24.131 r_dihedral_angle_3_deg 18.265 r_long_range_B_refined 13.653 r_long_range_B_other 13.652 r_scangle_other 10.934 r_mcangle_it 9.768 r_mcangle_other 9.767 r_scbond_it 7.96 r_scbond_other 7.959 r_mcbond_other 7.02 r_mcbond_it 7.019 r_dihedral_angle_1_deg 6.275 r_angle_refined_deg 1.877 r_angle_other_deg 1.376 r_chiral_restr 0.091 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4851 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms 224
Software Software Software Name Purpose REFMAC refinement Aimless data scaling iMOSFLM data reduction MOLREP phasing