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Ligand binding domain (LBD) of the p. aeruginosa nitrate receptor McpN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIQUID DIFFUSION 7.5 293 Capillary counterdiffusion method:
C23: 0.82 M K-phosphate, 0.82 M Na-phosphate, 0.1 M Na-Hepes pH 7.50
Crystal Properties Matthews coefficient Solvent content 2.66 53.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.777 α = 90 b = 87.949 β = 93.05 c = 52.896 γ = 90
Symmetry Space Group C 1 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 PIXEL DECTRIS PILATUS 6M-F Toroidal Mirror 2017-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.9724 ESRF ID23-1
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 1.3 46.32 85.43 0.0316 0.039 0.023 0.999 14.98 2.7 88758 17.09
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 1.3 1.35 92.43 0.3744 0.4657 0.2746 0.837 2.38 2.7
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 AB INITIO PHASING THROUGHOUT 1.3 46.32 84383 4375 85.44 0.12673 0.12535 0.1399 0.15325 0.167 RANDOM 23.273
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] -0.28 -0.14 0.11 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.287 r_sphericity_free 24.243 r_dihedral_angle_4_deg 15.866 r_dihedral_angle_3_deg 13.433 r_sphericity_bonded 11.515 r_dihedral_angle_1_deg 4.163 r_long_range_B_refined 3.359 r_long_range_B_other 3.285 r_scangle_other 2.608 r_mcangle_it 2.129
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.287 r_sphericity_free 24.243 r_dihedral_angle_4_deg 15.866 r_dihedral_angle_3_deg 13.433 r_sphericity_bonded 11.515 r_dihedral_angle_1_deg 4.163 r_long_range_B_refined 3.359 r_long_range_B_other 3.285 r_scangle_other 2.608 r_mcangle_it 2.129 r_mcangle_other 2.129 r_rigid_bond_restr 2.114 r_scbond_it 1.984 r_scbond_other 1.984 r_mcbond_it 1.642 r_mcbond_other 1.624 r_angle_refined_deg 1.4 r_angle_other_deg 0.796 r_chiral_restr 0.088 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2830 Nucleic Acid Atoms Solvent Atoms 429 Heterogen Atoms 32
Software Software Software Name Purpose PHENIX refinement REFMAC refinement XDS data reduction SCALA data scaling Arcimboldo phasing