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Crystal Structure of tudor domain of SMN1 in complex with a small organic molecule
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MHN pdb entry 1MHN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 293 2M ammonium sulfate, 0.2M potassium/sodium tartrate, 0.1M sodium citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.7 27.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 27.789 α = 90 b = 27.789 β = 90 c = 112.817 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 CCD RIGAKU SATURN A200 2014-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E 1.5418
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 1.75 37.61 100 0.078 19.8 10.5 5006
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 1.75 1.79 100 0.806 2.9 10.3 283
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 1MHN 1.75 24.07 4942 508 99.64 0.1727 0.1646 0.1779 0.2417 0.2506 RANDOM 26.6793
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] 0.67 0.33 0.67 -2.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.261 r_dihedral_angle_4_deg 17.7 r_dihedral_angle_3_deg 13.88 r_dihedral_angle_1_deg 6.883 r_mcangle_it 4.47 r_mcbond_it 3.213 r_mcbond_other 3.207 r_angle_refined_deg 1.653 r_angle_other_deg 0.874 r_chiral_restr 0.114
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.261 r_dihedral_angle_4_deg 17.7 r_dihedral_angle_3_deg 13.88 r_dihedral_angle_1_deg 6.883 r_mcangle_it 4.47 r_mcbond_it 3.213 r_mcbond_other 3.207 r_angle_refined_deg 1.653 r_angle_other_deg 0.874 r_chiral_restr 0.114 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 454 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 17
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction