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Crystal structure of mouse SNX25 RGS domain in space group P41212
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7WF8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 293 0.15M DL-Malic acid pH 7.0, 20%(w/v) Polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 3.09 60.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.877 α = 90 b = 70.877 β = 90 c = 148.539 γ = 90
Symmetry Space Group P 41 21 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 EIGER X 16M 2018-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.9792 SSRF BL17U1
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 2.55 74.27 99.5 0.058 0.062 0.022 0.998 13.7 7.8 12971
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 2.55 2.66 99.5 0.7 0.752 0.267 0.862 8.1
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 7WF8 2.55 20 12228 631 98.92 0.2248 0.2228 0.2297 0.2636 0.272 RANDOM 91.589
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] -2.83 -2.83 5.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.954 r_dihedral_angle_4_deg 22.622 r_dihedral_angle_3_deg 20.315 r_dihedral_angle_1_deg 7.048 r_angle_refined_deg 1.473 r_angle_other_deg 1.286 r_chiral_restr 0.08 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.954 r_dihedral_angle_4_deg 22.622 r_dihedral_angle_3_deg 20.315 r_dihedral_angle_1_deg 7.048 r_angle_refined_deg 1.473 r_angle_other_deg 1.286 r_chiral_restr 0.08 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2064 Nucleic Acid Atoms Solvent Atoms 2 Heterogen Atoms
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction DIALS data reduction MOLREP phasing