6GB8

Copper nitrite reductase from Achromobacter cycloclastes: small 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
2.0439.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.382α = 90
b = 96.382β = 90
c = 96.382γ = 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
11.4829.061000.9960.05711.755484988216.6
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)
11.481.511000.7260.87730.17206.5

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 REPLACEMENTTHROUGHOUT5i6k1.4829.0647321256199.980.18730.18580.2164RANDOM22.284
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_deg37.643
r_dihedral_angle_4_deg16.488
r_dihedral_angle_3_deg14.408
r_dihedral_angle_1_deg7.488
r_angle_other_deg3.828
r_mcangle_it2.109
r_angle_refined_deg1.641
r_mcbond_it1.332
r_mcbond_other1.331
r_chiral_restr0.091
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.643
r_dihedral_angle_4_deg16.488
r_dihedral_angle_3_deg14.408
r_dihedral_angle_1_deg7.488
r_angle_other_deg3.828
r_mcangle_it2.109
r_angle_refined_deg1.641
r_mcbond_it1.332
r_mcbond_other1.331
r_chiral_restr0.091
r_bond_refined_d0.013
r_gen_planes_other0.008
r_gen_planes_refined0.007
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2538
Nucleic Acid Atoms
Solvent Atoms137
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction
DIALSdata scaling
PHASERphasing