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A new bio-isosteric base pair based on reversible bonding
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XY5 PDB ENTRY 2XY5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 46-49% AMMONIUM SULFATE, 2-3% MPD, 100MM MES PH5.8
Crystal Properties Matthews coefficient Solvent content 3.28 62.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.442 α = 90 b = 93.996 β = 90 c = 105.416 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2013-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
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 70.16 99.6 0.08 22.05 8.8 59562 2
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 2.07 96.3 0.92 2.59 8.8
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 PDB ENTRY 2XY5 2 70.16 56624 2937 99.62 0.17977 0.17814 0.1898 0.21116 0.2192 RANDOM 34.73
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] 4.1 -2.23 -1.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.07 r_dihedral_angle_4_deg 18.478 r_dihedral_angle_3_deg 13.491 r_dihedral_angle_1_deg 5.824 r_scbond_it 4.362 r_mcangle_it 3.547 r_mcbond_it 2.9 r_mcbond_other 2.888 r_angle_refined_deg 1.663 r_angle_other_deg 1.138
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.07 r_dihedral_angle_4_deg 18.478 r_dihedral_angle_3_deg 13.491 r_dihedral_angle_1_deg 5.824 r_scbond_it 4.362 r_mcangle_it 3.547 r_mcbond_it 2.9 r_mcbond_other 2.888 r_angle_refined_deg 1.663 r_angle_other_deg 1.138 r_chiral_restr 0.106 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.007 r_gen_planes_other 0.001 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4538 Nucleic Acid Atoms 411 Solvent Atoms 210 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement XDS data reduction PHASER phasing