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Crystal structure of transcriptional regulator of TetR family (YP_425770.1) from Rhodospirillum rubrum ATCC 11170 at 1.50 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.79 293 NANODROP, 1.27M Ammonium sulfate, 0.1M MES pH 5.79, VAPOR DIFFUSION, SITTING DROP, temperature 293K 2 VAPOR DIFFUSION, SITTING DROP 5.64 293 NANODROP, 1.18M Ammonium sulfate, 0.1M MES pH 5.64, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.34 α = 90 b = 53.34 β = 90 c = 234.24 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 325 mm CCD Flat mirror (vertical focusing) 2008-04-03 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 315 1m long Rh coated bent cylindrical mirror for horizontal and vertical focusing 2008-03-23 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.97852 SSRL BL11-1 2 SYNCHROTRON SSRL BEAMLINE BL1-5 0.979137, 0.918381, 0.978532 SSRL BL1-5
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 1.5 29.285 98.3 0.036 17.05 59433 -3 20.454
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) 1.5 1.55 95.3 0.366 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.5 29.285 59383 3001 98.97 0.151 0.149 0.186 0.1975 RANDOM 19.055
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] 0.79 0.39 0.79 -1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.856 r_dihedral_angle_4_deg 17.683 r_dihedral_angle_3_deg 11.279 r_sphericity_free 7.645 r_scangle_it 6.71 r_scbond_it 5.159 r_sphericity_bonded 4.397 r_dihedral_angle_1_deg 3.342 r_mcangle_it 3.275 r_rigid_bond_restr 2.944
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.856 r_dihedral_angle_4_deg 17.683 r_dihedral_angle_3_deg 11.279 r_sphericity_free 7.645 r_scangle_it 6.71 r_scbond_it 5.159 r_sphericity_bonded 4.397 r_dihedral_angle_1_deg 3.342 r_mcangle_it 3.275 r_rigid_bond_restr 2.944 r_mcbond_it 2.195 r_angle_refined_deg 1.593 r_angle_other_deg 1.337 r_mcbond_other 1.201 r_chiral_restr 0.092 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2926 Nucleic Acid Atoms Solvent Atoms 327 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction MAR345 data collection ADSC data collection XDS data reduction SHELXD phasing autoSHARP phasing