6ZAU

Damage-free nitrite-bound copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) determined by serial femtosecond rotation crystallography


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6THF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP52911.6/1.8 M (NH4)2SO4 and 50mM HEPES buffer pH 5/ pH 5.5
Crystal Properties
Matthews coefficientSolvent content
2.656

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.95α = 90
b = 106.95β = 90
c = 106.95γ = 90
Symmetry
Space GroupP 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2020-02-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSACLA BEAMLINE BL21.2398SACLABL2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)R Split (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
11.375.6399.90.9510.1634.173.49987216.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)R Split (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.31.3599.50.0161.1261.4

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 REPLACEMENTTHROUGHOUT6THF1.329.899687503399.90.15830.15580.2061RANDOM22.613
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.631
r_dihedral_angle_4_deg20.814
r_dihedral_angle_3_deg13.402
r_dihedral_angle_1_deg8.361
r_rigid_bond_restr3.333
r_angle_refined_deg1.903
r_angle_other_deg1.514
r_chiral_restr0.104
r_bond_refined_d0.015
r_gen_planes_refined0.012
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.631
r_dihedral_angle_4_deg20.814
r_dihedral_angle_3_deg13.402
r_dihedral_angle_1_deg8.361
r_rigid_bond_restr3.333
r_angle_refined_deg1.903
r_angle_other_deg1.514
r_chiral_restr0.104
r_bond_refined_d0.015
r_gen_planes_refined0.012
r_gen_planes_other0.004
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2662
Nucleic Acid Atoms
Solvent Atoms459
Heterogen Atoms103

Software

Software
Software NamePurpose
REFMACrefinement
CrystFELdata reduction
XDSdata scaling
REFMACphasing