6HBE

Cu-containing nitrite reductase (NirK) from Thermus scotoductus SA-01


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3X1E 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52890.2 M CaCl2.2H2O, 0.1 M HEPES sodium pH: 7.5, 28% w/v PEG 400
Crystal Properties
Matthews coefficientSolvent content
2.448.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 145.692α = 90
b = 110.553β = 107.51
c = 88.81γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93PIXELDECTRIS PILATUS 6M2017-01-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.928190DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.6386.5198.40.0490.0490.0590.0320.99811.83.4163764
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)
11.631.721000.4540.5430.2950.8883.3

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 REPLACEMENTTHROUGHOUT3X1E1.6386.51155447831698.350.16270.16120.1901RANDOM29.474
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]
3.73-1.26-1.7-1.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.02
r_dihedral_angle_4_deg16.869
r_dihedral_angle_3_deg12.151
r_dihedral_angle_1_deg7.27
r_angle_refined_deg1.488
r_angle_other_deg0.935
r_chiral_restr0.096
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.02
r_dihedral_angle_4_deg16.869
r_dihedral_angle_3_deg12.151
r_dihedral_angle_1_deg7.27
r_angle_refined_deg1.488
r_angle_other_deg0.935
r_chiral_restr0.096
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9978
Nucleic Acid Atoms
Solvent Atoms853
Heterogen Atoms12

Software

Software
Software NamePurpose
XDSdata reduction
autoPROCdata scaling
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction