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Fragment of nitrate/nitrite sensor histidine kinase NarQ (WT) in asymmetric holo state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5IJI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 293 in meso lipidic cubic phase crystallization
Crystal Properties Matthews coefficient Solvent content 2.35 47.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.464 α = 90 b = 39.865 β = 100.62 c = 120.361 γ = 90
Symmetry Space Group P 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 2016-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.972 ESRF ID23-1
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 2.42 52.5 97.4 0.101 7.86 3.34 18994
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 2.42 2.5 89.8 0.832 1.62 3.33
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 THROUGHOUT 5IJI 2.42 52.5 17932 877 96.15 0.22087 0.2177 0.2249 0.28569 0.2939 RANDOM 50.419
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] 3.17 -2.87 2.62 -4.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.385 r_dihedral_angle_4_deg 21.514 r_dihedral_angle_3_deg 15.546 r_long_range_B_refined 9.381 r_long_range_B_other 9.38 r_scangle_other 7.349 r_mcangle_other 6.43 r_mcangle_it 6.429 r_scbond_it 4.759 r_scbond_other 4.758
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.385 r_dihedral_angle_4_deg 21.514 r_dihedral_angle_3_deg 15.546 r_long_range_B_refined 9.381 r_long_range_B_other 9.38 r_scangle_other 7.349 r_mcangle_other 6.43 r_mcangle_it 6.429 r_scbond_it 4.759 r_scbond_other 4.758 r_mcbond_it 4.347 r_mcbond_other 4.342 r_dihedral_angle_1_deg 3.88 r_angle_refined_deg 0.882 r_angle_other_deg 0.599 r_chiral_restr 0.047 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3388 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing