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THE SECOND C-KIT DNA QUADRUPLEX CRYSTAL STRUCTURE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QXR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 283 10% MPD, 10 MM MAGNESIUM CHLORIDE, 50
MM POTASSIUM CHLORIDE, AND 50 MM SODIUM CACODYLATE AT PH 6.5,
VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 283K
Crystal Properties Matthews coefficient Solvent content 1.87 34.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.85 α = 90 b = 94.85 β = 90 c = 30.363 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 105 CCD OXFORD ONYX CCD 2012-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9686 Diamond I04
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 2.73 28.48 94.4 0.115 5 2.6 2439
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-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 3QXR 2.73 28.48 2439 117 95.2 0.18504 0.18237 0.186 0.24332 0.2407 RANDOM 42.002
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] 0.3 0.15 0.3 -0.98
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 6.448 r_long_range_B_other 6.446 r_scangle_other 5.054 r_scbond_other 3.093 r_scbond_it 3.091 r_angle_other_deg 2.204 r_angle_refined_deg 1.281 r_chiral_restr 0.135 r_gen_planes_refined 0.01 r_bond_refined_d 0.008
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 6.448 r_long_range_B_other 6.446 r_scangle_other 5.054 r_scbond_other 3.093 r_scbond_it 3.091 r_angle_other_deg 2.204 r_angle_refined_deg 1.281 r_chiral_restr 0.135 r_gen_planes_refined 0.01 r_bond_refined_d 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg 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_mcangle_other 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 Nucleic Acid Atoms 938 Solvent Atoms 3 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PHASES phasing XIA data reduction