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Structural adaptation and conservation in quadruplex-drug recognition
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KF1 PDB ENTRY 1KF1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 283 300mM sodium chloride, 50mM sodium cacodylate pH 6.5, 30% v/v MPD, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Crystal Properties Matthews coefficient Solvent content 3.14 60.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.35 α = 90 b = 61.35 β = 90 c = 43.63 γ = 120
Symmetry Space Group P 64 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 210 MONOCHROMATOR 2007-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.9785 ESRF ID14-1
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 1.97 22.69 98.9 0.056 23.3 10 3739 3697 33
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) 1.97 2.04 100 0.134 10.8 10.8 359
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 1KF1 2.2 10 2520 2520 123 98.8 0.25664 0.25664 0.25436 0.2486 0.30275 0.2971 RANDOM 21.26
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] 1.39 0.7 1.39 -2.09
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 3.389 r_angle_refined_deg 3.306 r_scbond_it 1.92 r_symmetry_vdw_refined 0.397 r_nbd_refined 0.394 r_nbtor_refined 0.353 r_xyhbond_nbd_refined 0.318 r_metal_ion_refined 0.232 r_symmetry_hbond_refined 0.179 r_chiral_restr 0.138
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 3.389 r_angle_refined_deg 3.306 r_scbond_it 1.92 r_symmetry_vdw_refined 0.397 r_nbd_refined 0.394 r_nbtor_refined 0.353 r_xyhbond_nbd_refined 0.318 r_metal_ion_refined 0.232 r_symmetry_hbond_refined 0.179 r_chiral_restr 0.138 r_symmetry_metal_ion_refined 0.101 r_bond_refined_d 0.019 r_gen_planes_refined 0.019 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_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 219 Solvent Atoms 28 Heterogen Atoms 130
Software Software Software Name Purpose REFMAC refinement ADSC data collection d*TREK data reduction d*TREK data scaling PHASER phasing