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Crystal structure of transcriptional regulator, MarR family, from Silicibacter pomeroyi
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 281 0.1 Succinic acid pH 7.0, 12 % PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 281K
Crystal Properties Matthews coefficient Solvent content 2.26 45.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.976 α = 90 b = 87.976 β = 90 c = 43.197 γ = 90
Symmetry Space Group P 43 21 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 ADSC QUANTUM 315 2007-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97935 APS 19-ID
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 1.95 50 100 0.094 77.2 21 12944 12941 -3 28
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 1.95 2.02 100 0.472 14.5 21.8 1263
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 (All) 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 SAD THROUGHOUT 1.95 43.98 12819 12819 624 99.2 0.18119 0.18119 0.17912 0.1782 0.22257 0.2249 RANDOM 32.927
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] -0.75 -0.75 1.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.835 r_dihedral_angle_4_deg 17.392 r_dihedral_angle_3_deg 12.965 r_dihedral_angle_1_deg 5.126 r_scangle_it 2.881 r_scbond_it 2.006 r_mcangle_it 1.329 r_angle_refined_deg 1.282 r_mcbond_it 0.857 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.835 r_dihedral_angle_4_deg 17.392 r_dihedral_angle_3_deg 12.965 r_dihedral_angle_1_deg 5.126 r_scangle_it 2.881 r_scbond_it 2.006 r_mcangle_it 1.329 r_angle_refined_deg 1.282 r_mcbond_it 0.857 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.266 r_nbd_refined 0.21 r_symmetry_hbond_refined 0.176 r_xyhbond_nbd_refined 0.132 r_chiral_restr 0.098 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 1133 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing