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Structure of the effector-binding domain of deoxyribonucleoside regulator DeoR from Bacillus subtilis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OQP PDB ENTRY 4OQP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 0.1 M Bicine, 20% (w/v) PEG 6000; 12.5 mg/mL protein in 20 mM trisodium citrate pH 7.0, 150 mM NaCl, 0.02% (v/v) 2-mercaptoethanol; protein:reservoir 1:2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.94 58.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.081 α = 90 b = 63.081 β = 90 c = 150.129 γ = 120
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-soated silicon and glass mirrors 2012-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.9184 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 1.8 50 93.1 0.048 3.8 62177 57887
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 1.8 1.86 53.3 0.179 2.9 2.6
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 4OQP 1.8 27.31 62177 54842 2921 92.87 0.19455 0.19276 0.2027 0.22756 0.2332 RANDOM 52.488
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.194 r_dihedral_angle_4_deg 16.52 r_dihedral_angle_3_deg 12.636 r_long_range_B_refined 6.277 r_long_range_B_other 6.276 r_dihedral_angle_1_deg 5.788 r_scangle_other 2.851 r_mcangle_it 2.234 r_mcangle_other 2.072 r_scbond_it 2.014
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.194 r_dihedral_angle_4_deg 16.52 r_dihedral_angle_3_deg 12.636 r_long_range_B_refined 6.277 r_long_range_B_other 6.276 r_dihedral_angle_1_deg 5.788 r_scangle_other 2.851 r_mcangle_it 2.234 r_mcangle_other 2.072 r_scbond_it 2.014 r_scbond_other 1.863 r_mcbond_it 1.513 r_mcbond_other 1.513 r_angle_refined_deg 1.439 r_angle_other_deg 0.79 r_chiral_restr 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 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 3970 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms 22
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling