6XYN

Crystal structure of a proteolytic fragment of NarQ comprising sensor and TM domains


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE2951 M KH2PO4/Na2HPO4 pH 5.2 and 5 mM NaNO3
Crystal Properties
Matthews coefficientSolvent content
3.3663.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.283α = 90
b = 51.283β = 90
c = 182.988γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-11-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.9724ESRFID23-1

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.349.3897.80.0640.0730.0350.99913.24.310245
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)RedundancyNumber Unique Reflections (All)
12.32.3899.80.5540.6320.2990.7724.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5IJI2.349.38973351297.710.25070.2490.2848RANDOM70.04
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]
-0.49-0.490.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.774
r_dihedral_angle_4_deg13.389
r_dihedral_angle_3_deg12.123
r_dihedral_angle_1_deg3.384
r_angle_refined_deg0.677
r_angle_other_deg0.521
r_chiral_restr0.04
r_bond_refined_d0.004
r_gen_planes_refined0.003
r_bond_other_d
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.774
r_dihedral_angle_4_deg13.389
r_dihedral_angle_3_deg12.123
r_dihedral_angle_1_deg3.384
r_angle_refined_deg0.677
r_angle_other_deg0.521
r_chiral_restr0.04
r_bond_refined_d0.004
r_gen_planes_refined0.003
r_bond_other_d
r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1243
Nucleic Acid Atoms
Solvent Atoms81
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing