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Crystal structure of Bacillus subtilis PadR in complex with operator DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5X12
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 1.4 M ammonium sulfate, 0.1 M MES, 0.2 M lithium sulfate
Crystal Properties Matthews coefficient Solvent content 2.9 57.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 341.807 α = 90 b = 61.567 β = 107.94 c = 120.553 γ = 90
Symmetry Space Group C 1 2 1
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 270 2015-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 1.00003 PAL/PLS 7A (6B, 6C1)
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 2.65 30 99.4 0.064 31.1 3.6 69940
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 2.65 2.7 0.521
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 5X12 2.65 30 66237 3328 99.33 0.23012 0.22817 0.2248 0.26819 0.2631 RANDOM
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] -5.09 -2 5.69 -1.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.58 r_dihedral_angle_3_deg 16.631 r_dihedral_angle_4_deg 15.482 r_dihedral_angle_1_deg 4.621 r_scangle_it 1.575 r_angle_refined_deg 1.274 r_scbond_it 0.975 r_mcangle_it 0.483 r_mcbond_it 0.241 r_chiral_restr 0.071
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.58 r_dihedral_angle_3_deg 16.631 r_dihedral_angle_4_deg 15.482 r_dihedral_angle_1_deg 4.621 r_scangle_it 1.575 r_angle_refined_deg 1.274 r_scbond_it 0.975 r_mcangle_it 0.483 r_mcbond_it 0.241 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other 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 11121 Nucleic Acid Atoms 2284 Solvent Atoms 17 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing