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Crystal structure of the overoxidized AbfR bound to DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HBL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 100 mM sodium cacodylate, 100 mM NaCl, 50 mM Mg2Cl, 12% PEG 5000
Crystal Properties Matthews coefficient Solvent content 2.88 57.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.305 α = 90 b = 290.914 β = 90 c = 52.351 γ = 90
Symmetry Space Group P 21 21 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 315r 2012-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9735 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3 50 94.2 23.3 4.9 43913
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.05
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 4HBL 3 30 42122 2236 93.79 0.22648 0.22393 0.2297 0.27235 0.2814 RANDOM 75.168
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] 6.8 -6.85 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.136 r_dihedral_angle_4_deg 19.595 r_dihedral_angle_3_deg 17.642 r_long_range_B_other 9.524 r_long_range_B_refined 9.523 r_scangle_other 7.254 r_mcangle_it 7.059 r_mcangle_other 7.059 r_dihedral_angle_1_deg 5.476 r_scbond_it 4.739
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.136 r_dihedral_angle_4_deg 19.595 r_dihedral_angle_3_deg 17.642 r_long_range_B_other 9.524 r_long_range_B_refined 9.523 r_scangle_other 7.254 r_mcangle_it 7.059 r_mcangle_other 7.059 r_dihedral_angle_1_deg 5.476 r_scbond_it 4.739 r_scbond_other 4.738 r_mcbond_it 4.66 r_mcbond_other 4.659 r_angle_refined_deg 1.49 r_angle_other_deg 1.169 r_chiral_restr 0.079 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9037 Nucleic Acid Atoms 3912 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing