☰ Navigation Tabs
RNA-activated 2-AIpG monomer complex, 2h soaking
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DHC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291 10% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.040 M Sodium cacodylate trihydrate pH 7.0, 0.012 M Spermine tetrahydrochloride, 0.080 M Sodium chloride, 0.020 M Magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.73 55.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.975 α = 90 b = 46.975 β = 90 c = 83.097 γ = 120
Symmetry Space Group P 3 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 99 CCD MAR CCD 130 mm 2016-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1 ALS 8.2.2
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 1.9 50 91.6 0.079 0.083 0.027 0.966 24.5 9 8006
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 1.9 1.97 47.2 0.567 0.617 0.236 0.868 1.35 5.1
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 5dhc 1.9 50 7516 405 90.26 0.24923 0.24586 0.251 0.30635 0.3024 RANDOM 38.258
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] -0.02
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 4.799 r_long_range_B_other 4.786 r_scangle_other 4.318 r_angle_other_deg 4.1 r_scbond_it 3.075 r_scbond_other 3.074 r_angle_refined_deg 2.66 r_chiral_restr 0.181 r_bond_other_d 0.066 r_bond_refined_d 0.025
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 4.799 r_long_range_B_other 4.786 r_scangle_other 4.318 r_angle_other_deg 4.1 r_scbond_it 3.075 r_scbond_other 3.074 r_angle_refined_deg 2.66 r_chiral_restr 0.181 r_bond_other_d 0.066 r_bond_refined_d 0.025 r_gen_planes_refined 0.012 r_gen_planes_other 0.002 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 644 Solvent Atoms 30 Heterogen Atoms 166
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing