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A parallel stranded human telomeric quadruplex in complex with the porphyrin TMPyP4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2A5R PDB ENTRY 2A5R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 285 500 mM ammonium sulphate, 80 mM lithium sulphate, 80 mM sodium chloride, 80 mM potassium chloride, 20mM potassium cacodylate, pH 6.5, VAPOR DIFFUSION, temperature 285K
Crystal Properties Matthews coefficient Solvent content 2.47 50.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.29 α = 90 b = 61.99 β = 90 c = 61.4 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 105 IMAGE PLATE RIGAKU RAXIS IV osmic mirrors 2006-06-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 2.09 28.35 99.9 0.043 18.2 5.07 4443 4443 45
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 2.09 2.16 99.5 0.201 6.5 4.9 433
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 (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 PDB ENTRY 2A5R 2.09 28.35 4239 4239 204 99.82 0.20062 0.20062 0.19829 0.194 0.24833 0.2231 RANDOM 24.671
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] -2.19 2.06 0.13
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 2.577 r_angle_refined_deg 2.16 r_scbond_it 1.874 r_nbd_refined 0.322 r_nbtor_refined 0.308 r_symmetry_hbond_refined 0.262 r_symmetry_vdw_refined 0.249 r_xyhbond_nbd_refined 0.173 r_metal_ion_refined 0.107 r_chiral_restr 0.092
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 2.577 r_angle_refined_deg 2.16 r_scbond_it 1.874 r_nbd_refined 0.322 r_nbtor_refined 0.308 r_symmetry_hbond_refined 0.262 r_symmetry_vdw_refined 0.249 r_xyhbond_nbd_refined 0.173 r_metal_ion_refined 0.107 r_chiral_restr 0.092 r_gen_planes_refined 0.017 r_bond_refined_d 0.013 r_bond_other_d r_angle_other_deg r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_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 462 Solvent Atoms 46 Heterogen Atoms 107
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction d*TREK data scaling PHASER phasing