5OF5 | pdb_00005of5

Cu nitrite reductase serial data at varying temperatures


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5298100 mM sodium citrate at pH 5.0 and ~1.7 M ammonium sulphate
Crystal Properties
Matthews coefficientSolvent content
1.9536.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.94α = 90
b = 94.94β = 90
c = 94.94γ = 90
Symmetry
Space GroupP 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray190PIXELDECTRIS PILATUS 6M-F2015-12-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.99SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim I (All)CC (Half)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
11.0842.4699.40.0290.9913.75.91208358
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.081.193.90.6230.321.13.1

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5I6K1.0842.46114845594999.340.117260.115950.120.143270.14RANDOM12.26
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_deg35.109
r_sphericity_free20.261
r_dihedral_angle_4_deg18.613
r_dihedral_angle_3_deg11.763
r_dihedral_angle_1_deg7.779
r_sphericity_bonded6.28
r_rigid_bond_restr4.132
r_long_range_B_refined2.905
r_long_range_B_other2.905
r_scangle_other2.456
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2581
Nucleic Acid Atoms
Solvent Atoms436
Heterogen Atoms61

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing