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Transcription repressor NrdR from E. coli, AMPPNP/ATP-bound state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7P3Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Protein at 8 mg/ml in 1.5 mM ADP, 1.1 mM AMPPNP, 25 mM Tris-HCl pH 9 (at 277 K), 300 mM NaCl, 1 mM TCEP, 10 mM MgCl2. 150 nL protein were mixed with with 50 nL reservoir solution containing 0.1 M Bis-Tris propane pH 7.5, 0.2 M potassium thiocyanate, 20% (w/v) PEG3350 at 293 K. Crystals were harvested in paraffin oil.
Crystal Properties Matthews coefficient Solvent content 2.74 55.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.797 α = 90 b = 129.791 β = 90 c = 143.877 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER X 16M 2021-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.97963 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.331 96.372 75.7 0.204 0.212 0.057 0.996 10 13.7 51826
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.331 2.569 15.1 2.451 2.547 0.687 0.427 1.5 13.6
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 MOLECULAR REPLACEMENT THROUGHOUT 2.331 96.37 51826 2573 75.7 0.2259 0.2243 0.2565 0.2285 RANDOM 64.13
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] -0.0244 0.673 -0.6486
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.65 t_omega_torsion 2.5 t_angle_deg 0.86 t_bond_d 0.007 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9669 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms 504
Software Software Software Name Purpose BUSTER refinement XDS data scaling autoPROC data reduction PHASER phasing