2XAO

Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from A. thaliana in complex with 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 3300, 100 MM BIS-TRIS PH 5.9, 2 MM MGCL2. PROTEIN WAS MIXED WITH 2 MM INOSITOL-5-P
Crystal Properties
Matthews coefficientSolvent content
2.347.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.761α = 90
b = 112.737β = 90
c = 144.454γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120CCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-2ESRFID23-2

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
12.788.741000.134.246.9222033257
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)
12.93.061000.451.666.99

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2XAM2.988.73621980114199.9950.2280.22490.2907RANDOM38.993
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]
0.267-1.7161.449
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.168
r_dihedral_angle_3_deg20.117
r_dihedral_angle_4_deg19.598
r_dihedral_angle_1_deg5.543
r_scangle_it1.847
r_angle_refined_deg1.371
r_scbond_it1.067
r_mcangle_it0.937
r_mcbond_it0.524
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.168
r_dihedral_angle_3_deg20.117
r_dihedral_angle_4_deg19.598
r_dihedral_angle_1_deg5.543
r_scangle_it1.847
r_angle_refined_deg1.371
r_scbond_it1.067
r_mcangle_it0.937
r_mcbond_it0.524
r_nbtor_refined0.306
r_nbd_refined0.216
r_symmetry_vdw_refined0.215
r_xyhbond_nbd_refined0.145
r_chiral_restr0.09
r_symmetry_hbond_refined0.086
r_metal_ion_refined0.063
r_bond_refined_d0.01
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6602
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling