4CO0

Structure of PII signaling protein GlnZ from Azospirillum brasilense in complex with adenosine diphosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4CNYPDB ENTRY 4CNY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52931 MM MNCL2, 5MM 2OG, 5 MMATP, 0.2 M K/NA TARTRATE, 200% PEG 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
1.9135.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.55α = 90
b = 86.55β = 90
c = 65.13γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MVERTICALLY COLLIMATING MIRROR FOLLOWED BY A BARTELS MONOCHROMATOR AND TOROIDAL MIRROR2009-06-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DASLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.429.87980.0812.85.4351242
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.599.80.523.25.33

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 4CNY1.429.8681.9935124175797.990.21220.21050.245323.09
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]
-0.4369-0.43690.8739
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d16.881
f_angle_d1.178
f_chiral_restr0.072
f_bond_d0.005
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1596
Nucleic Acid Atoms
Solvent Atoms271
Heterogen Atoms64

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing