☰ Navigation Tabs
Crystal Structure of the Gemin2-binding domain of SMN, Gemin2dN39 in Complex with SmD1(1-82)/D2/F/E from Human
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3S6N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 4% PEG8000, 100mM Tris.HCl
Crystal Properties Matthews coefficient Solvent content 3.98 69.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.17 α = 90 b = 114.09 β = 90 c = 125.39 γ = 90
Symmetry Space Group P 21 21 21
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 MARMOSAIC 225 mm CCD 2016-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97853 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.37 60 100 12.9 10.8 17350
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 3S6N 3.38 60 13841 728 84.25 0.1886 0.1855 0.1905 0.2485 0.2483 RANDOM 76.05
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] 0.12 0.03 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.153 r_dihedral_angle_3_deg 21.828 r_dihedral_angle_4_deg 19.381 r_dihedral_angle_1_deg 7.535 r_angle_refined_deg 1.624 r_angle_other_deg 0.817 r_chiral_restr 0.075 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.153 r_dihedral_angle_3_deg 21.828 r_dihedral_angle_4_deg 19.381 r_dihedral_angle_1_deg 7.535 r_angle_refined_deg 1.624 r_angle_other_deg 0.817 r_chiral_restr 0.075 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4346 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data collection SCALEPACK data scaling PDB_EXTRACT data extraction DENZO data reduction PHASER phasing