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Crystal structure of a proteolytic fragment of NarQ comprising sensor and TM domains
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 295 1 M KH2PO4/Na2HPO4 pH 5.2 and 5 mM NaNO3
Crystal Properties Matthews coefficient Solvent content 3.36 63.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.283 α = 90 b = 51.283 β = 90 c = 182.988 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-F 2015-11-20 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 2.3 49.38 97.8 0.064 0.073 0.035 0.999 13.2 4.3 10245
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 2.3 2.38 99.8 0.554 0.632 0.299 0.772 4.4
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 2.3 49.38 9733 512 97.71 0.2507 0.249 0.2525 0.2848 0.2867 RANDOM 70.04
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] -0.49 -0.49 0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.774 r_dihedral_angle_4_deg 13.389 r_dihedral_angle_3_deg 12.123 r_dihedral_angle_1_deg 3.384 r_angle_refined_deg 0.677 r_angle_other_deg 0.521 r_chiral_restr 0.04 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.774 r_dihedral_angle_4_deg 13.389 r_dihedral_angle_3_deg 12.123 r_dihedral_angle_1_deg 3.384 r_angle_refined_deg 0.677 r_angle_other_deg 0.521 r_chiral_restr 0.04 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1243 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction MOLREP phasing