6QPX

Crystal structure of nitrite bound Y323A 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
Matthew coefficientSolvent content
2.7455

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 128.5α = 90
b = 128.5β = 90
c = 172.47γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2018-07-27MSINGLE 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)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
11.6130.199.80.1420.0710.997513723414.878
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)
11.611.6499.91.80.890.4485

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 DIFFRACTIONTHROUGHOUT1.729.33111132544799.750.175180.17380.20303RANDOM20.427
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]
0.190.10.19-0.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.057
r_dihedral_angle_4_deg21.566
r_dihedral_angle_3_deg13.037
r_dihedral_angle_1_deg7.266
r_long_range_B_refined5.98
r_long_range_B_other5.461
r_scangle_other1.838
r_angle_refined_deg1.509
r_angle_other_deg1.363
r_mcangle_it1.228
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.057
r_dihedral_angle_4_deg21.566
r_dihedral_angle_3_deg13.037
r_dihedral_angle_1_deg7.266
r_long_range_B_refined5.98
r_long_range_B_other5.461
r_scangle_other1.838
r_angle_refined_deg1.509
r_angle_other_deg1.363
r_mcangle_it1.228
r_mcangle_other1.228
r_scbond_it1.13
r_scbond_other1.129
r_mcbond_it0.74
r_mcbond_other0.737
r_chiral_restr0.067
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_gen_planes_other0.004
r_bond_other_d0.001
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_scangle_it
r_metal_ion_refined
r_metal_ion_other
r_sphericity_bonded
r_rigid_bond_restr
r_sphericity_free
r_symmetry_vdw_refined
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6839
Nucleic Acid Atoms
Solvent Atoms1174
Heterogen Atoms96

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
REFMACphasing