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RNA-dGMP complex with Sr ion
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 Strontium chloride
Crystal Properties Matthews coefficient Solvent content 2.8 56.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.707 α = 90 b = 48.707 β = 90 c = 80.58 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 2017-10-25 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) 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 2.5 50 97.5 0.096 13.1 4.5 4047
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 2.5 2.59 82 0.44 1.96 3.1
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 2.5 50 3729 176 93.9 0.218 0.215 0.2295 0.28 0.2824 RANDOM 73.72
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] 0.05 0.03 0.05 -0.16
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 10.573 r_long_range_B_refined 10.495 r_scangle_other 8.801 r_scbond_it 6.306 r_scbond_other 6.125 r_angle_other_deg 4.212 r_angle_refined_deg 2.668 r_chiral_restr 0.167 r_bond_other_d 0.043 r_bond_refined_d 0.021
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 10.573 r_long_range_B_refined 10.495 r_scangle_other 8.801 r_scbond_it 6.306 r_scbond_other 6.125 r_angle_other_deg 4.212 r_angle_refined_deg 2.668 r_chiral_restr 0.167 r_bond_other_d 0.043 r_bond_refined_d 0.021 r_gen_planes_refined 0.009 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 8 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing