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GpppA dinucleotide ligand binding to RNA UC template
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HBX PDB entry 5HBX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 0.02 M magnesium chloride hexahydrate, 0.05 M MOPS, pH 7.0, 55% v/v Tacsimate, pH 7.0, 2 mM hexammine cobalt(III) chloride
Crystal Properties Matthews coefficient Solvent content 2.45 53.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.121 α = 90 b = 44.121 β = 90 c = 84.53 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 2022-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.987 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.64 50 90.1 0.136 0.976 10.8 10.1 10994
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.64 1.7 100 0.796 0.985 8.1 10.4
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 PDB entry 5HBX 1.64 28.19 10409 556 89.8 0.24945 0.24802 0.2519 0.2745 0.2834 RANDOM 35.887
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 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 7.189 r_long_range_B_other 7.189 r_angle_other_deg 4.561 r_scangle_other 4.469 r_angle_refined_deg 3.845 r_scbond_it 3.279 r_scbond_other 3.278 r_chiral_restr 0.352 r_bond_other_d 0.026 r_bond_refined_d 0.023
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 7.189 r_long_range_B_other 7.189 r_angle_other_deg 4.561 r_scangle_other 4.469 r_angle_refined_deg 3.845 r_scbond_it 3.279 r_scbond_other 3.278 r_chiral_restr 0.352 r_bond_other_d 0.026 r_bond_refined_d 0.023 r_gen_planes_refined 0.019 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 598 Solvent Atoms 31 Heterogen Atoms 102
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing