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Crystal structure of Putative TetR-family transcriptional regulator (YP_752756.1) from Syntrophomonas wolfei str. Goettingen at 2.07 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.3 277 25.0000% Ethylene-Glycol, No Buffer pH 4.3, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.15 42.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.184 α = 90 b = 68.184 β = 90 c = 75.71 γ = 120
Symmetry Space Group P 32 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 MARMOSAIC 325 mm CCD Flat collimating mirror, toroid focusing mirror 2010-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 SSRL BL9-2
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 2.07 59.05 99 0.078 17.45 12714 -3 42.439
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 2.07 2.14 96.3 0.013 2.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.07 59.05 12714 620 99.24 0.19 0.188 0.1943 0.234 0.2434 RANDOM 29.327
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] 0.35 0.18 0.35 -0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.894 r_dihedral_angle_4_deg 21.194 r_dihedral_angle_3_deg 14.091 r_scangle_it 7.134 r_scbond_it 5.179 r_dihedral_angle_1_deg 4.741 r_mcangle_it 2.946 r_mcbond_it 1.806 r_angle_refined_deg 1.434 r_angle_other_deg 0.928
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.894 r_dihedral_angle_4_deg 21.194 r_dihedral_angle_3_deg 14.091 r_scangle_it 7.134 r_scbond_it 5.179 r_dihedral_angle_1_deg 4.741 r_mcangle_it 2.946 r_mcbond_it 1.806 r_angle_refined_deg 1.434 r_angle_other_deg 0.928 r_mcbond_other 0.518 r_chiral_restr 0.078 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1562 Nucleic Acid Atoms Solvent Atoms 65 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELXD phasing autoSHARP phasing