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Crystal Structure of the Gemin2-binding domain of SMN, Gemin2 in Complex with SmD1(1-82)/D2/F/E/G 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 6% PEG8000, 100mM Tris.HCl
Crystal Properties Matthews coefficient Solvent content 3.53 65.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.32 α = 90 b = 115.76 β = 90 c = 128.21 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 2015-12-14 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 3.28 60 99 13.6 12.4 19335
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 3.28 60 14695 775 79.17 0.2013 0.1981 0.2049 0.2618 0.2647 RANDOM 85.217
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] -1.3 -0.1 1.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.448 r_dihedral_angle_3_deg 21.96 r_dihedral_angle_4_deg 18.714 r_dihedral_angle_1_deg 7.463 r_angle_refined_deg 1.54 r_angle_other_deg 0.807 r_chiral_restr 0.073 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.448 r_dihedral_angle_3_deg 21.96 r_dihedral_angle_4_deg 18.714 r_dihedral_angle_1_deg 7.463 r_angle_refined_deg 1.54 r_angle_other_deg 0.807 r_chiral_restr 0.073 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4793 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