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Crystal Structure of UP1 Complexed With d(TTAGGGTT PRN GGG); A Human Telomeric Repeat Containing nebularine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2UP1 PDB ENTRY 2UP1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.1 283 ammonium phosphate, glycerol, Tris, sodium chloride, MES, EDTA, beta-mercaptoethanol , pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 283.0K
Crystal Properties Matthews coefficient Solvent content 2.266 44.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.853 α = 90 b = 50.853 β = 90 c = 172.962 γ = 90
Symmetry Space Group P 43 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 103 CCD RIGAKU JUPITER osmic mirrors 2001-10-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2 20 91.2 0.062 0.062 9.9 2.91 16172 14752 25.7
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) 2 2.07 87.1 0.47 1.7 2.36 1222
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 2UP1 2 19.9 16172 14752 734 91.2 0.233 0.233 0.2361 0.274 0.2758 RANDOM 29.9
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] 5.96 5.96 -11.92
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.9 c_scangle_it 2.92 c_mcangle_it 2.17 c_scbond_it 1.99 c_mcbond_it 1.37 c_improper_angle_d 1.27 c_angle_deg 1.1 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.9 c_scangle_it 2.92 c_mcangle_it 2.17 c_scbond_it 1.99 c_mcbond_it 1.37 c_improper_angle_d 1.27 c_angle_deg 1.1 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1466 Nucleic Acid Atoms 230 Solvent Atoms 118 Heterogen Atoms
Software Software Software Name Purpose CNS refinement CrystalClear data reduction d*TREK data scaling CNS phasing