6QQ2

Crystal structure of nitrite bound Y323F mutant of haem-Cu containing nitrite reductase from Ralstonia pickettii


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52840.1M HEPES (pH7.5), 20% PEG 3350, 0.2 M Sodium citrate
Crystal Properties
Matthews coefficientSolvent content
4.9675

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 180.975α = 90
b = 180.975β = 90
c = 180.975γ = 90
Symmetry
Space GroupI 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6Mmirrors2018-12-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.9686DiamondI24

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.673.8892.90.1380.1040.9735.52.92790936.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.72970.6340.4960.5481.82.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONTHROUGHOUT2.67326486142391.780.153790.151920.18876RANDOM40.4
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.686
r_dihedral_angle_4_deg20.853
r_dihedral_angle_3_deg16.19
r_long_range_B_refined8.237
r_long_range_B_other8.214
r_dihedral_angle_1_deg7.85
r_scangle_other6.667
r_mcangle_it4.886
r_mcangle_other4.886
r_scbond_it4.477
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.686
r_dihedral_angle_4_deg20.853
r_dihedral_angle_3_deg16.19
r_long_range_B_refined8.237
r_long_range_B_other8.214
r_dihedral_angle_1_deg7.85
r_scangle_other6.667
r_mcangle_it4.886
r_mcangle_other4.886
r_scbond_it4.477
r_scbond_other4.472
r_mcbond_it3.316
r_mcbond_other3.293
r_angle_refined_deg1.74
r_angle_other_deg1.266
r_chiral_restr0.067
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_gen_planes_other0.004
r_bond_other_d0.001
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 AtomsNumber
Protein Atoms3424
Nucleic Acid Atoms
Solvent Atoms221
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing