2XAN

inositol 1,3,4,5,6-pentakisphosphate 2-kinase from A. thaliana in complex with AMP PNP and IP5


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2XAMPDB ENTRY 2XAM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.922% PEG 3350, 100 MM BIS-TRIS, PH 5.9 PROTEIN WAS MIXED WITH 2 MM AMP PNP AND 2 MM INOSITOL-5-P
Crystal Properties
Matthews coefficientSolvent content
2.346

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.418α = 90
b = 113.429β = 90
c = 140.472γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120CCDADSC CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
12.288.2599.60.16.17.64724729.1
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)
12.22.3299.60.461.67.6

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2XAM2.2140.0344857238999.480.226930.224270.220.277390.27RANDOM21.19
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]
0.07-0.960.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.994
r_dihedral_angle_4_deg17.684
r_dihedral_angle_3_deg15.798
r_dihedral_angle_1_deg5.258
r_scangle_it2.039
r_scbond_it1.218
r_angle_refined_deg1.095
r_mcangle_it0.867
r_mcbond_it0.456
r_chiral_restr0.064
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6590
Nucleic Acid Atoms
Solvent Atoms259
Heterogen Atoms130

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing