6QPZ

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


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52830.1M HEPES (pH7.5), 20% PEG 3350, 0.2 M Sodium citrate
Crystal Properties
Matthews coefficientSolvent content
2.7555

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 127.55α = 90
b = 127.55β = 90
c = 172.68γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6Mmirrors2018-04-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.97857SOLEILPROXIMA 1

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
11.4546.6498.50.0540.050.998.82.8183931
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)
11.451.4995.21.1670.9050.4280.82.5

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 DIFFRACTIONTHROUGHOUT1.6542.73118437623498.850.159370.158380.17806RANDOM20.555
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]
0.830.420.83-2.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.145
r_dihedral_angle_4_deg21.092
r_dihedral_angle_3_deg12.668
r_dihedral_angle_1_deg7.302
r_long_range_B_refined5.851
r_long_range_B_other5.499
r_scangle_other2.074
r_angle_refined_deg1.671
r_angle_other_deg1.45
r_mcangle_it1.283
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.145
r_dihedral_angle_4_deg21.092
r_dihedral_angle_3_deg12.668
r_dihedral_angle_1_deg7.302
r_long_range_B_refined5.851
r_long_range_B_other5.499
r_scangle_other2.074
r_angle_refined_deg1.671
r_angle_other_deg1.45
r_mcangle_it1.283
r_mcangle_other1.283
r_scbond_it1.282
r_scbond_other1.282
r_mcbond_it0.773
r_mcbond_other0.773
r_chiral_restr0.077
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6859
Nucleic Acid Atoms
Solvent Atoms1165
Heterogen Atoms96

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing