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Structure of chicken LGP2 witha 5'p 10-mer dsRNA and ADP-AlF4-Mg.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TMI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 5prime monophosphate 10-mer dsRNA:ADP:AlF4:mg complex was mixed with reservoir buffer (0.1 M tri-sodium citrate dihydrate pH 6.1, 0.04-0.08 M ammonium dihydrogen phosphate) in a 2:1 ratio.
Crystal Properties Matthews coefficient Solvent content 2.47 50.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.59 α = 90 b = 97.05 β = 90 c = 122.52 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 PIXEL DECTRIS PILATUS3 6M 2014-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.9786 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.5 76.1 99.9 0.048 17.6 5.25 132907
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 1.5 1.55 99.8 0.746 2.31 5.27
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 3TMI 1.5 76.08 126226 6681 99.87 0.13483 0.13305 0.133 0.16847 0.1684 RANDOM 29.159
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 -0.62 -0.38
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 36.294 r_dihedral_angle_2_deg 33.296 r_dihedral_angle_4_deg 18.634 r_sphericity_bonded 14.583 r_dihedral_angle_3_deg 13.321 r_dihedral_angle_1_deg 5.826 r_long_range_B_refined 5.578 r_long_range_B_other 5.276 r_scangle_other 4.929 r_scbond_it 4.252
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 36.294 r_dihedral_angle_2_deg 33.296 r_dihedral_angle_4_deg 18.634 r_sphericity_bonded 14.583 r_dihedral_angle_3_deg 13.321 r_dihedral_angle_1_deg 5.826 r_long_range_B_refined 5.578 r_long_range_B_other 5.276 r_scangle_other 4.929 r_scbond_it 4.252 r_scbond_other 4.252 r_mcangle_it 3.658 r_mcangle_other 3.657 r_mcbond_other 2.991 r_mcbond_it 2.99 r_rigid_bond_restr 2.681 r_angle_refined_deg 1.51 r_angle_other_deg 1.014 r_chiral_restr 0.095 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5228 Nucleic Acid Atoms 448 Solvent Atoms 563 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing