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Fragment of nitrate/nitrite sensor histidine kinase NarQ (R50K) in symmetric apo 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 2.63 53.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.593 α = 90 b = 59.366 β = 90 c = 239.583 γ = 90
Symmetry Space Group I 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 PILATUS 6M-F 2016-04-03 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) 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 1.9 47.64 99.8 0.067 0.998 13.77 6.42 22889
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 1.9 2 99.9 1.23 1.42 6.72
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 1.9 47.64 21742 1148 99.85 0.23424 0.23175 0.245 0.28498 0.2995 RANDOM 50.078
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] 5.1 1.27 -6.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.454 r_dihedral_angle_3_deg 15.811 r_dihedral_angle_4_deg 14.875 r_long_range_B_refined 12.103 r_long_range_B_other 12.027 r_scangle_other 9.512 r_mcangle_it 7.355 r_mcangle_other 7.354 r_scbond_it 6.727 r_scbond_other 6.436
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.454 r_dihedral_angle_3_deg 15.811 r_dihedral_angle_4_deg 14.875 r_long_range_B_refined 12.103 r_long_range_B_other 12.027 r_scangle_other 9.512 r_mcangle_it 7.355 r_mcangle_other 7.354 r_scbond_it 6.727 r_scbond_other 6.436 r_mcbond_it 5.151 r_mcbond_other 5.12 r_dihedral_angle_1_deg 4.041 r_angle_refined_deg 1.018 r_angle_other_deg 0.633 r_chiral_restr 0.052 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 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 1749 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing