6GCG

Copper nitrite reductase from Achromobacter cycloclastes: large polymorph dataset 15


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
2.1542.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.989α = 90
b = 97.989β = 90
c = 97.989γ = 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
11.829.551000.9990.05830.729782932115.5148580083
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)
11.81.831000.5020.6910.06799

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 REPLACEMENTFREE R-VALUE5i6k1.8001524415429.54464438822932115811000.1683744794020.1662352839040.205036675018RANDOM27.7443443621
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
f_dihedral_angle_d12.3900597213
f_angle_d0.884836202221
f_chiral_restr0.0577525434176
f_bond_d0.00630526667572
f_plane_restr0.00557028246372
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2534
Nucleic Acid Atoms
Solvent Atoms113
Heterogen Atoms2

Software

Software
Software NamePurpose
DIALSdata reduction
REFMACrefinement
PHENIXrefinement
PHASERphasing