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Structure of the C13.18 RNA Aptamer in Complex with G Protein-Coupled Receptor Kinase 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OMW Chain A OF PDB ENTRY 1OMW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.9 277 100 mM MES pH 5.9, 100 mM NaCl and 5% PEG 3350 supplemented with 0.1 M glycine, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.82 56.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.346 α = 90 b = 139.719 β = 90 c = 60.949 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD RAYONIX MX-300 2010-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 3.5 50 65.5 0.103 28.9 7.8 8251 -3
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 3.5 3.56 14.8 0.49 4.7 8.3 92
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 Chain A OF PDB ENTRY 1OMW 3.51 24.88 -1000000000000000000 7811 7811 382 64.54 0.22035 0.22035 0.21582 0.2238 0.31691 0.3217 RANDOM 129.331
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] -0.11 1 -0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.688 r_dihedral_angle_3_deg 16.516 r_dihedral_angle_4_deg 10.722 r_dihedral_angle_1_deg 6.483 r_angle_refined_deg 0.909 r_angle_other_deg 0.759 r_chiral_restr 0.053 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.688 r_dihedral_angle_3_deg 16.516 r_dihedral_angle_4_deg 10.722 r_dihedral_angle_1_deg 6.483 r_angle_refined_deg 0.909 r_angle_other_deg 0.759 r_chiral_restr 0.053 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scbond_it 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 4809 Nucleic Acid Atoms 125 Solvent Atoms Heterogen Atoms 1
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling