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Crystal Structure of the Gemin2-binding domain of SMN, Gemin2 in Complex with SmD1(1-82)/D2.R61A/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 1% PEG8000, 100mM Tris.HCl
Crystal Properties Matthews coefficient Solvent content 2.29 46.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.64 α = 90 b = 84.76 β = 90 c = 114.33 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 2015-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.97846 SSRF BL17U1
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 2.92 66.98 99.6 8.6 12 13784
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 2.92 66.98 11984 632 70.16 0.2027 0.1987 0.2034 0.2806 0.2786 RANDOM 63.778
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] 0.04 -0.04 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.164 r_dihedral_angle_3_deg 23.344 r_dihedral_angle_4_deg 19.548 r_dihedral_angle_1_deg 6.913 r_angle_refined_deg 1.42 r_angle_other_deg 0.813 r_chiral_restr 0.068 r_bond_refined_d 0.01 r_bond_other_d 0.006 r_gen_planes_refined 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.164 r_dihedral_angle_3_deg 23.344 r_dihedral_angle_4_deg 19.548 r_dihedral_angle_1_deg 6.913 r_angle_refined_deg 1.42 r_angle_other_deg 0.813 r_chiral_restr 0.068 r_bond_refined_d 0.01 r_bond_other_d 0.006 r_gen_planes_refined 0.005 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4919 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