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Mechanism for regulation of DNA binding of Bordetella bronchiseptica BpsR by 6-hydroxynicotinic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NNN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 285 18% PEG 2250, 0.2 M potassium formate, and 15% butanediol
Crystal Properties Matthews coefficient Solvent content 1.93 36.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.87 α = 90 b = 90.523 β = 90 c = 103.051 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 CCD RIGAKU SATURN 92 VariMax 2012-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.65 34.03 98.65 0.058 0.068 0.034 0.999 23.4 1.1 17964 70.01
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.75 2.85 97.44 0.549 0.642 0.33 0.906 4.38 1.1
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 2NNN 2.75 34.03 16513 895 96.44 0.23479 0.23116 0.2323 0.30139 0.3007 RANDOM 71.499
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] -0.18 -0.08 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.812 r_dihedral_angle_4_deg 18.431 r_dihedral_angle_3_deg 13.686 r_long_range_B_other 11.132 r_long_range_B_refined 11.131 r_scangle_other 9.257 r_mcangle_it 8.027 r_mcangle_other 8.025 r_dihedral_angle_1_deg 6.628 r_scbond_it 6.345
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.812 r_dihedral_angle_4_deg 18.431 r_dihedral_angle_3_deg 13.686 r_long_range_B_other 11.132 r_long_range_B_refined 11.131 r_scangle_other 9.257 r_mcangle_it 8.027 r_mcangle_other 8.025 r_dihedral_angle_1_deg 6.628 r_scbond_it 6.345 r_scbond_other 6.323 r_mcbond_it 5.542 r_mcbond_other 5.536 r_angle_refined_deg 1.217 r_angle_other_deg 0.91 r_chiral_restr 0.06 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3512 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing