☰ Navigation Tabs
RNA duplex with 2-MeImpG analogue bound-one binding site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HBX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 1.8305 M Malonic acid, 0.25 M Ammonium citrate tribasic, 0.12 M Succinic acid, 0.3 M DL-Malic acid, 0.4 M Sodium acetate trihydrate, 0.5 M Sodium formate, and 0.16 M Ammonium tartrate dibasic, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.2 44.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.852 α = 90 b = 42.852 β = 90 c = 83.841 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 ADSC QUANTUM 315 2016-01-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1 ALS 8.2.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.9 50 97.4 0.137 0.115 0.957 10.04 7.3 7273
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.97 95.4 0.468 0.434 0.9 2.94 4.2
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 5HBX 1.9 37.11 6924 348 97 0.22942 0.22737 0.2334 0.27244 0.2778 RANDOM 43.859
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 9.162 r_long_range_B_refined 9.152 r_scangle_other 6.548 r_scbond_other 4.652 r_scbond_it 4.651 r_angle_other_deg 3.945 r_angle_refined_deg 2.686 r_chiral_restr 0.133 r_bond_other_d 0.073 r_bond_refined_d 0.026
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 9.162 r_long_range_B_refined 9.152 r_scangle_other 6.548 r_scbond_other 4.652 r_scbond_it 4.651 r_angle_other_deg 3.945 r_angle_refined_deg 2.686 r_chiral_restr 0.133 r_bond_other_d 0.073 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 644 Solvent Atoms 3 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing