6GBB

Copper nitrite reductase from Achromobacter cycloclastes: large cell polymorph dataset 1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5I6K 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE4.5298Batch microcrystals were prepared by rapidly mixing 20 mg/ml AcNiR in 20mM Tris, pH 7.5 with a solution containing 2.5 M ammonium sulphate, 0.1 M sodium citrate pH 4.5 buffer, in a ratio of 1:3 and mixed by vortexing for 60 seconds. Microcrystals with a diameter of 5-15 microns grew at room temperature over a period of 4-6 days.
Crystal Properties
Matthews coefficientSolvent content
2.1342.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.747α = 90
b = 97.747β = 90
c = 97.747γ = 90
Symmetry
Space GroupP 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298PIXELDECTRIS PILATUS3 6M2018-01-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.9686DiamondI24

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
11.4829.471000.99460.07431.573585198118.4
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)
11.481.511000.4870.8110.12137

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 REPLACEMENTTHROUGHOUT5I6K1.4829.4749430255199.940.20560.20450.2277RANDOM23.28
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_deg36.543
r_dihedral_angle_4_deg22.524
r_dihedral_angle_3_deg12.81
r_dihedral_angle_1_deg7.325
r_angle_other_deg3.814
r_mcangle_it2.068
r_angle_refined_deg1.623
r_mcbond_it1.318
r_mcbond_other1.31
r_chiral_restr0.088
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.543
r_dihedral_angle_4_deg22.524
r_dihedral_angle_3_deg12.81
r_dihedral_angle_1_deg7.325
r_angle_other_deg3.814
r_mcangle_it2.068
r_angle_refined_deg1.623
r_mcbond_it1.318
r_mcbond_other1.31
r_chiral_restr0.088
r_bond_refined_d0.012
r_gen_planes_other0.008
r_gen_planes_refined0.007
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2539
Nucleic Acid Atoms
Solvent Atoms118
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction
DIALSdata scaling
PHASERphasing