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Structure of the effector-binding domain of arabinose repressor AraR from Bacillus subtilis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JFT PDB entry 1JFT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 arabinose 50mM at 16.8mg/ml, 70mM HEPES pH7.5, 7% PEG8000, 6% ethylene glycol, 20% glycerol, 10mM spermidine, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.76 55.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.068 α = 90 b = 106.333 β = 90 c = 111.847 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 MARMOSAIC 225 mm CCD double crystal monochromator with 2 sets of Rh-coated mirrors 2011-01-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.917 BESSY 14.2
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 2.2 30 86.8 0.57 35.9 66 38046 33024
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 2.28 59.6 0.28 4.9 5.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1JFT 2.21 29.91 36080 31295 1660 86.74 0.18808 0.1857 0.1834 0.23099 0.2275 RANDOM 51.952
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] 9.13 -5.41 -3.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.783 r_dihedral_angle_4_deg 18.205 r_dihedral_angle_3_deg 17.525 r_dihedral_angle_1_deg 6.613 r_scangle_it 1.95 r_angle_refined_deg 1.452 r_scbond_it 1.276 r_mcangle_it 0.737 r_mcbond_it 0.451 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.783 r_dihedral_angle_4_deg 18.205 r_dihedral_angle_3_deg 17.525 r_dihedral_angle_1_deg 6.613 r_scangle_it 1.95 r_angle_refined_deg 1.452 r_scbond_it 1.276 r_mcangle_it 0.737 r_mcbond_it 0.451 r_nbtor_refined 0.3 r_nbd_refined 0.206 r_symmetry_hbond_refined 0.171 r_xyhbond_nbd_refined 0.154 r_symmetry_vdw_refined 0.149 r_chiral_restr 0.096 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4459 Nucleic Acid Atoms Solvent Atoms 245 Heterogen Atoms 32
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling