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Crystal structure of the MarR family transcriptional regulator SPO1453 from Silicibacter pomeroyi DSS-3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 289 2.0M Ammonium sulfate, 0.1M Citrate pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 4.42 72.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.14 α = 90 b = 124.14 β = 90 c = 140.186 γ = 120
Symmetry Space Group P 62 2 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 APS-1 Mirrors 2007-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.9793 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.69 35.37 99.5 0.115 0.115 7.2 11.9 18036 18036 -3 55.32
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.69 2.8 94.2 0.835 0.835 2.6 12.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.69 35.37 17960 17960 915 98.42 0.20154 0.20019 0.22748 0.2047 RANDOM 54.7
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] -0.69 -0.34 -0.69 1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.829 r_dihedral_angle_3_deg 21.75 r_dihedral_angle_4_deg 20.544 r_scangle_it 5.421 r_dihedral_angle_1_deg 5.213 r_mcangle_it 3.919 r_scbond_it 3.281 r_mcbond_it 2.268 r_angle_refined_deg 1.623 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.829 r_dihedral_angle_3_deg 21.75 r_dihedral_angle_4_deg 20.544 r_scangle_it 5.421 r_dihedral_angle_1_deg 5.213 r_mcangle_it 3.919 r_scbond_it 3.281 r_mcbond_it 2.268 r_angle_refined_deg 1.623 r_nbtor_refined 0.311 r_symmetry_hbond_refined 0.31 r_symmetry_vdw_refined 0.26 r_nbd_refined 0.253 r_xyhbond_nbd_refined 0.18 r_chiral_restr 0.103 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 2093 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms 48
Software Software Software Name Purpose HKL-3000 phasing MLPHARE phasing DM model building SHELXD phasing RESOLVE model building Coot model building REFMAC refinement SBC-Collect data collection HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling DM phasing RESOLVE phasing