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RNA primer-template complex with 2-methylimidazole-activated monomer analogue-2 binding sites
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, SITTING DROP 7.5 292 Ammonium acetate, Magnesium chloride hexahydrate,0.05 M TRIS hydrochloride pH 7.5,10% v/v (+/-)-2-Methyl-2,4-pentanediol
Crystal Properties Matthews coefficient Solvent content 2.39 52.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.545 α = 90 b = 43.545 β = 90 c = 83.996 γ = 120
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 MAR CCD 165 mm 2015-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 0.987 ALS 8.2.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.7 50 99.9 0.128 14.6 7.4 19566 19566 0.05 0.05
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 1.7 1.76 100 0.488 2.64 5.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1.7 50 0.05 18463 1103 99.82 0.21478 0.21292 0.2192 0.24899 0.2553 RANDOM 29.324
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 8.695 r_long_range_B_refined 8.675 r_scangle_other 5.728 r_angle_other_deg 3.869 r_scbond_it 3.73 r_scbond_other 3.729 r_angle_refined_deg 2.77 r_chiral_restr 0.122 r_bond_other_d 0.041 r_bond_refined_d 0.026
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 8.695 r_long_range_B_refined 8.675 r_scangle_other 5.728 r_angle_other_deg 3.869 r_scbond_it 3.73 r_scbond_other 3.729 r_angle_refined_deg 2.77 r_chiral_restr 0.122 r_bond_other_d 0.041 r_bond_refined_d 0.026 r_gen_planes_refined 0.018 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 1188 Solvent Atoms 91 Heterogen Atoms 232
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing