☰ Navigation Tabs
Crystal structure of an RNA aptamer bound to human thrombin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PPB PDB ENTRY 1PPB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 290 PEG 8000, Magnesium Acetate, Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.98 58.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.766 α = 90 b = 134.017 β = 90 c = 44.033 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 98 IMAGE PLATE RIGAKU RAXIS IV Yale mirrors 2002-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.9 50 93.2 0.054 37211 -3 14.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.97 70 0.354
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT PDB ENTRY 1PPB 1.9 30.35 35581 1764 89 0.204 0.1925 0.254 0.2391 RANDOM 38.6
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] -13.01 23.88 -10.87
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 27.1 c_scangle_it 3.02 c_mcangle_it 2.21 c_scbond_it 2.06 c_mcbond_it 1.43 c_angle_deg 1.4 c_improper_angle_d 1.15 c_bond_d 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2328 Nucleic Acid Atoms 537 Solvent Atoms 253 Heterogen Atoms 96
Software Software Software Name Purpose CNS refinement PDB_EXTRACT data extraction DENZO data reduction SCALEPACK data scaling CNS phasing