6GBY

Copper nitrite reductase from Achromobacter cycloclastes: non-polymorph separated 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 2.5M ammonium sulphate, 0.1M sodium citrate pH 4.5 - in a ratio of 1:3 and mixed by vortexing for 60s. Microcrystals with a diameter of 5-15 microns grew at room temperature over a periof of 4-6 days
Crystal Properties
Matthews coefficientSolvent content
2.1342.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.87α = 90
b = 96.87β = 90
c = 96.87γ = 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
11.4829.211000.9970.05151.8892750616
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)
11.481.511000.5520.5450.15302

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 REPLACEMENTTHROUGHOUT5i6k1.4829.2148121247499.970.23710.235060.27645RANDOM24.407
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_deg36.956
r_dihedral_angle_4_deg20.758
r_dihedral_angle_3_deg16.451
r_dihedral_angle_1_deg7.788
r_long_range_B_refined4.399
r_long_range_B_other4.392
r_scangle_other2.784
r_mcangle_it2.165
r_mcangle_other2.164
r_scbond_it1.764
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.956
r_dihedral_angle_4_deg20.758
r_dihedral_angle_3_deg16.451
r_dihedral_angle_1_deg7.788
r_long_range_B_refined4.399
r_long_range_B_other4.392
r_scangle_other2.784
r_mcangle_it2.165
r_mcangle_other2.164
r_scbond_it1.764
r_scbond_other1.759
r_angle_refined_deg1.598
r_mcbond_it1.366
r_mcbond_other1.364
r_angle_other_deg0.965
r_chiral_restr0.09
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2541
Nucleic Acid Atoms
Solvent Atoms117
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
DIALSdata scaling