6QQ0

Crystal structure of nitrite bound Y323E mutant of haem-Cu containing nitrite reductase from Ralstonia pickettii


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2840.1M HEPES (pH7.5), 20% PEG 3350, 0.2 M Sodium citrate
Crystal Properties
Matthews coefficientSolvent content
2.7255

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 127.65α = 90
b = 127.65β = 90
c = 86.56γ = 120
Symmetry
Space GroupH 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 I240.96861DiamondI24

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
11.46199.70.0720.0580.9966.82.810329613.5
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)
11.41.4299.61.160.910.3040.82.8

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 DIFFRACTIONTHROUGHOUT1.446.6397927536999.680.115150.113450.1458RANDOM19.905
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]
0.410.20.41-1.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.969
r_dihedral_angle_4_deg20.588
r_dihedral_angle_3_deg12.416
r_dihedral_angle_1_deg7.232
r_long_range_B_refined5.023
r_long_range_B_other4.5
r_scangle_other3.817
r_scbond_it3.317
r_scbond_other3.317
r_mcangle_it2.631
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.969
r_dihedral_angle_4_deg20.588
r_dihedral_angle_3_deg12.416
r_dihedral_angle_1_deg7.232
r_long_range_B_refined5.023
r_long_range_B_other4.5
r_scangle_other3.817
r_scbond_it3.317
r_scbond_other3.317
r_mcangle_it2.631
r_mcangle_other2.63
r_rigid_bond_restr2.494
r_mcbond_it2.04
r_mcbond_other2.032
r_angle_refined_deg1.67
r_angle_other_deg1.469
r_chiral_restr0.088
r_bond_refined_d0.012
r_gen_planes_refined0.011
r_gen_planes_other0.006
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_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3432
Nucleic Acid Atoms
Solvent Atoms506
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
REFMACphasing