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Structure of the R. erythropolis transcriptional repressor QsdR from TetR family
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Phasing from S-SAD model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 20% 2-Methyl-2,4-pentanediol, 0.2 M CaCl2, 0.1 M Na Acetate pH 4.5
Crystal Properties Matthews coefficient Solvent content 3.58 65.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.63 α = 90 b = 91.63 β = 90 c = 145.22 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2013-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.980110 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.97 50 99.9 0.086 12.44 6.7 42157 34.16
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.97 2.09 99.3 0.902 1.86 6.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT FREE R-VALUE Phasing from S-SAD model 1.97 45.81 42146 2107 99.9 0.2071 0.206 0.171 0.2281 0.1949 RANDOM 40.21
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] -4.5943 -4.5943 9.1885
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.41 t_omega_torsion 2.58 t_angle_deg 1.03 t_bond_d 0.009 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.41 t_omega_torsion 2.58 t_angle_deg 1.03 t_bond_d 0.009 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2902 Nucleic Acid Atoms Solvent Atoms 317 Heterogen Atoms 58
Software Software Software Name Purpose BUSTER refinement PHASER phasing XDS data reduction XDS data scaling