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The structural basis for recognition of J-base containing DNA by a novel DNA-binding domain in JBP1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 20MM HEPES PH 7.5, 50MM NACL, 1MM TCEP 15.3% PEG 6000, 0.2M POTASSIUM NITRATE, 20% GLYCEROL (CRYO-PROTECTANT)
Crystal Properties Matthews coefficient Solvent content 2.83 56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.338 α = 90 b = 67.338 β = 90 c = 186.762 γ = 120
Symmetry Space Group P 61 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 77 PIXEL DECTRIS PILATUS 6M 2010-03-20 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 1.9 20 99.7 0.09 10.9 5.2 20683 1 36
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 1.9 2 98.3 0.66 2.3 5.4
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 SAD THROUGHOUT NONE 1.9 58.32 19541 1055 99.58 0.17553 0.1742 0.189 0.20038 0.2137 RANDOM 45.111
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] 0.66 0.33 0.66 -0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.578 r_dihedral_angle_4_deg 16.458 r_dihedral_angle_3_deg 13.07 r_dihedral_angle_1_deg 4.386 r_angle_refined_deg 1.255 r_angle_other_deg 0.888 r_symmetry_vdw_refined 0.349 r_nbd_refined 0.258 r_symmetry_vdw_other 0.195 r_nbtor_refined 0.174
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.578 r_dihedral_angle_4_deg 16.458 r_dihedral_angle_3_deg 13.07 r_dihedral_angle_1_deg 4.386 r_angle_refined_deg 1.255 r_angle_other_deg 0.888 r_symmetry_vdw_refined 0.349 r_nbd_refined 0.258 r_symmetry_vdw_other 0.195 r_nbtor_refined 0.174 r_nbd_other 0.17 r_xyhbond_nbd_refined 0.118 r_nbtor_other 0.085 r_chiral_restr 0.082 r_mcangle_it 0.073 r_mcbond_it 0.058 r_symmetry_hbond_refined 0.02 r_mcbond_other 0.016 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_it 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 1320 Nucleic Acid Atoms Solvent Atoms 164 Heterogen Atoms 10
Software Software Software Name Purpose XDS data reduction SCALA data scaling PHENIX.HYSS phasing PHASER phasing REFMAC refinement