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Crystal structure of transcriptional regulator of the TetR/AcrR family (YP_290855.1) from THERMOBIFIDA FUSCA YX-ER1 at 2.50 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 277 31.0% 2-methyl-2,4-pentanediol, 0.2M sodium chloride, 0.1M TRIS pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.29 46.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.87 α = 90 b = 67.62 β = 104.23 c = 72.98 γ = 90
Symmetry Space Group P 1 21 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 mirror (vertical focusing) 2008-05-13 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.97968,0.97917,0.91837 SSRL BL11-1
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 2.5 29.074 93.6 0.047 11.12 15426 -3 49.009
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) 2.5 2.59 81.3 0.352 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 MAD THROUGHOUT 2.5 29.074 15414 772 97.85 0.243 0.241 0.2428 0.277 0.2708 RANDOM 36.112
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] 0.15 -0.78 -0.41 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.887 r_dihedral_angle_3_deg 12.45 r_dihedral_angle_4_deg 9.972 r_scangle_it 3.259 r_dihedral_angle_1_deg 3.086 r_scbond_it 2.317 r_angle_refined_deg 1.438 r_angle_other_deg 1.284 r_mcangle_it 1.144 r_mcbond_it 0.846
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.887 r_dihedral_angle_3_deg 12.45 r_dihedral_angle_4_deg 9.972 r_scangle_it 3.259 r_dihedral_angle_1_deg 3.086 r_scbond_it 2.317 r_angle_refined_deg 1.438 r_angle_other_deg 1.284 r_mcangle_it 1.144 r_mcbond_it 0.846 r_nbd_refined 0.15 r_nbtor_refined 0.144 r_mcbond_other 0.135 r_nbd_other 0.118 r_xyhbond_nbd_refined 0.1 r_symmetry_vdw_other 0.098 r_chiral_restr 0.081 r_nbtor_other 0.069 r_symmetry_vdw_refined 0.055 r_symmetry_hbond_refined 0.055 r_bond_refined_d 0.016 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2978 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SOLVE phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction