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Crystal structure of DNA duplex containing ZP base pair
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 463D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 20 mM Sodium Cacodylate, pH 7.0
600 mM Calcium chloride
50% hexylene glycol
Crystal Properties Matthews coefficient Solvent content 2.44 49.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.7 α = 90 b = 41.7 β = 90 c = 99.932 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 63 PIXEL DECTRIS PILATUS 2M 2013-05-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.987 Diamond I04-1
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 2.17 33.96 99.21 0.066 15.1 9.6 3244
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 2.17 2.24 97.4 0.495 3.6 7.9
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 463D 2.17 33.96 3244 148 99.21 0.2223 0.2197 0.2236 0.2746 0.2745 RANDOM 59.206
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] 0.04 0.02 0.04 -0.14
RMS Deviations Key Refinement Restraint Deviation r_scbond_it 5.804 r_angle_refined_deg 1.704 r_angle_other_deg 1.672 r_chiral_restr 0.085 r_gen_planes_refined 0.016 r_bond_refined_d 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 460 Solvent Atoms 5 Heterogen Atoms 4
Software Software Software Name Purpose Aimless data scaling MOSFLM data reduction PHASER phasing REFMAC refinement PDB_EXTRACT data extraction