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Crystal structure of Gemin5 WD40 repeats in complex with m7GpppG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5TEE apo GEMIN5 WD40 repeats
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.5 293 15% PEG4000, 0.2 M ammonium acetate, 0.1 sodium citrate, 0.0005-0.001 M m7GpppG
Crystal Properties Matthews coefficient Solvent content 2.35 47.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.658 α = 90 b = 124.862 β = 117.52 c = 60.938 γ = 90
Symmetry Space Group P 1 21 1
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 300 mm CCD 2011-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.97944 APS 23-ID-B
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 1.95 48.02 98.6 0.079 0.092 0.046 0.997 11 3.9 55703
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 1.95 2 97.6 0.675 0.781 0.393 0.847 1.8 3.9 3879
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT "apo" GEMIN5 WD40 repeats 1.95 48.02 52871 2802 98.4 0.1807 0.1787 0.1881 0.2174 0.2241 34.097
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] 1.14 -0.71 -3.16 1.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.285 r_dihedral_angle_4_deg 13.895 r_dihedral_angle_3_deg 12.8 r_dihedral_angle_1_deg 6.914 r_mcangle_it 4.677 r_mcbond_it 3.317 r_mcbond_other 3.317 r_angle_refined_deg 1.524 r_angle_other_deg 0.943 r_chiral_restr 0.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.285 r_dihedral_angle_4_deg 13.895 r_dihedral_angle_3_deg 12.8 r_dihedral_angle_1_deg 6.914 r_mcangle_it 4.677 r_mcbond_it 3.317 r_mcbond_other 3.317 r_angle_refined_deg 1.524 r_angle_other_deg 0.943 r_chiral_restr 0.088 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5186 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing