2J9E | pdb_00002j9e

Structure of GlnK1 with bound effectors indicates regulatory mechanism for ammonia uptake


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2J9CPDB ENTRY 2J9C

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.6pH 4.60
Crystal Properties
Matthews coefficientSolvent content
2.4249.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.4α = 90
b = 77.8β = 90
c = 82.2γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2005-12-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SASLSX10SA

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
11.630920.0327.89.4477048.6
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)
11.61.757.70.168.66.5

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-Work (Depositor)R-Free (Depositor)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2J9C1.6219.894530823851000.1440.1420.19RANDOM20.48
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]
0.470.03-0.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.794
r_dihedral_angle_3_deg14.982
r_dihedral_angle_4_deg11.44
r_scangle_it6.01
r_dihedral_angle_1_deg5.872
r_scbond_it4.208
r_mcangle_it3.364
r_mcbond_it2.193
r_angle_refined_deg1.636
r_angle_other_deg0.939
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2688
Nucleic Acid Atoms
Solvent Atoms392
Heterogen Atoms113

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing