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Sequence specific recognition of RNA hairpins by the SAM domain of Vts1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2D3D PDB Entry: 2D3D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 2.5 M Ammonium sulfate,
50 mM MES pH 5.5,
10 mM Magnesium Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.62 53.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 27.55 α = 90 b = 44.53 β = 90 c = 129.23 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 IMAGE PLATE RIGAKU RAXIS IV 2005-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-002 1.54
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 2 64.55 99.9 0.057 11.37 6.4 11366 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.1 99.9 0.139 6.43 5.7 1523
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB Entry: 2D3D 2 64.55 11388 11366 789 99.84 0.231 0.23 0.228 0.2313 0.277 0.2828 RANDOM 26.027
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] -0.22 0.37 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.636 r_dihedral_angle_4_deg 16.707 r_dihedral_angle_3_deg 15.855 r_dihedral_angle_1_deg 4.659 r_scangle_it 1.595 r_angle_refined_deg 1.319 r_scbond_it 1.055 r_mcangle_it 0.701 r_mcbond_it 0.407 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.636 r_dihedral_angle_4_deg 16.707 r_dihedral_angle_3_deg 15.855 r_dihedral_angle_1_deg 4.659 r_scangle_it 1.595 r_angle_refined_deg 1.319 r_scbond_it 1.055 r_mcangle_it 0.701 r_mcbond_it 0.407 r_nbtor_refined 0.298 r_nbd_refined 0.197 r_xyhbond_nbd_refined 0.189 r_symmetry_hbond_refined 0.148 r_symmetry_vdw_refined 0.137 r_chiral_restr 0.069 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 672 Nucleic Acid Atoms 317 Solvent Atoms 117 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction CrystalClear data reduction XDS data scaling PHASER phasing