6QPT

Crystal structure of nitrite bound synthetic core domain of nitrite reductase from Ralstonia pickettii (residues 1-331)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62840.2 MgCl2, 20% P6000 in MES buffer pH 6.0
Crystal Properties
Matthews coefficientSolvent content
2.3547.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 165.91α = 90
b = 167.553β = 90
c = 143.973γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16MMirrors2018-10-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.91587DiamondI04-1

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
11.898399.90.210.090.995.36.7515919834.11
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)
11.891.9299.71.250.520.4850.96.57

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.950.01149138756699.860.180480.178340.22377RANDOM26.74
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]
0.02-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.116
r_dihedral_angle_4_deg19.889
r_dihedral_angle_3_deg13.391
r_dihedral_angle_1_deg8.689
r_long_range_B_refined4.53
r_long_range_B_other4.53
r_angle_refined_deg1.373
r_angle_other_deg1.259
r_scangle_other1.217
r_mcangle_it1.042
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.116
r_dihedral_angle_4_deg19.889
r_dihedral_angle_3_deg13.391
r_dihedral_angle_1_deg8.689
r_long_range_B_refined4.53
r_long_range_B_other4.53
r_angle_refined_deg1.373
r_angle_other_deg1.259
r_scangle_other1.217
r_mcangle_it1.042
r_mcangle_other1.041
r_scbond_it0.732
r_scbond_other0.732
r_mcbond_it0.616
r_mcbond_other0.615
r_chiral_restr0.056
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms14602
Nucleic Acid Atoms
Solvent Atoms1849
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
MOLREPphasing