6QPV

Crystal structure of as isolated Y323A mutant of haem-Cu containing nitrite reductase from Ralstonia pickettii


X-RAY DIFFRACTION

Starting Model(s)

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

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
2.7455.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 128.23α = 90
b = 128.23β = 90
c = 172.65γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2018-03-02MSINGLE 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
11.543.8399.90.1520.0680.9968.34.8169421
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.531001.2270.650.65514.5

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 REPLACEMENTTHROUGHOUT3ziy1.642.83132598706099.920.166960.165450.19587RANDOM17.483
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]
-0.2-0.1-0.20.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.009
r_dihedral_angle_4_deg21.03
r_dihedral_angle_3_deg12.589
r_dihedral_angle_1_deg7.319
r_long_range_B_refined5.706
r_long_range_B_other5.223
r_scangle_other3.279
r_scbond_other2.115
r_scbond_it2.114
r_mcangle_it1.806
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.009
r_dihedral_angle_4_deg21.03
r_dihedral_angle_3_deg12.589
r_dihedral_angle_1_deg7.319
r_long_range_B_refined5.706
r_long_range_B_other5.223
r_scangle_other3.279
r_scbond_other2.115
r_scbond_it2.114
r_mcangle_it1.806
r_mcangle_other1.806
r_angle_refined_deg1.592
r_angle_other_deg1.431
r_mcbond_it1.212
r_mcbond_other1.211
r_chiral_restr0.076
r_bond_refined_d0.01
r_gen_planes_refined0.01
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 Atoms6844
Nucleic Acid Atoms
Solvent Atoms1290
Heterogen Atoms90

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
REFMACphasing