6QPU

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


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6297containing 0.2 MgCl2, 20% P6000 in MES buffer pH 6.0
Crystal Properties
Matthew coefficientSolvent content
2.3547.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 165.884α = 90
b = 167.52β = 90
c = 143.982γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER R 4M2018-09-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.54

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
12.2545.694.40.110.0760.9949.33.88491225.5
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)
12.252.375.40.750.530.5411.43.4

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 REPLACEMENTTHROUGHOUT3ziy2.2542.6884912442694.120.18170.178840.23698RANDOM30.131
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]
0.58-1.120.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.405
r_dihedral_angle_4_deg19.23
r_dihedral_angle_3_deg15.26
r_dihedral_angle_1_deg9.075
r_long_range_B_other3.529
r_long_range_B_refined3.528
r_scangle_other1.728
r_mcangle_it1.486
r_mcangle_other1.485
r_angle_refined_deg1.443
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.405
r_dihedral_angle_4_deg19.23
r_dihedral_angle_3_deg15.26
r_dihedral_angle_1_deg9.075
r_long_range_B_other3.529
r_long_range_B_refined3.528
r_scangle_other1.728
r_mcangle_it1.486
r_mcangle_other1.485
r_angle_refined_deg1.443
r_angle_other_deg1.203
r_scbond_other1
r_scbond_it0.999
r_mcbond_it0.869
r_mcbond_other0.869
r_chiral_restr0.059
r_gen_planes_refined0.006
r_bond_refined_d0.006
r_gen_planes_other0.001
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 Atoms14615
Nucleic Acid Atoms
Solvent Atoms1062
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing