4O4B

Crystal Structure of an Inositol hexakisphosphate kinase EhIP6KA as a fusion protein with maltose binding protein


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1EZ9PDB ENTRIES 1EZ9 AND 1W2C
experimental modelPDB 1W2CPDB ENTRIES 1EZ9 AND 1W2C

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.529112% (w/v) PEG 3350, 50 mM NaH2PO4, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.4549.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.626α = 90
b = 51.98β = 90
c = 117.328γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2013-02-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.0APS22-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.85099.40.05739.6567725677253
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8399.40.4573.14.83301

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRIES 1EZ9 AND 1W2C1.836.976410464104338398.660.197440.197440.196180.22102RANDOM35.793
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]
-0.23-0.190.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.361
r_dihedral_angle_4_deg13.413
r_dihedral_angle_3_deg13.181
r_long_range_B_refined9.271
r_long_range_B_other9.156
r_dihedral_angle_1_deg5.444
r_mcangle_it1.486
r_mcangle_other1.486
r_scangle_other1.42
r_angle_refined_deg1.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.361
r_dihedral_angle_4_deg13.413
r_dihedral_angle_3_deg13.181
r_long_range_B_refined9.271
r_long_range_B_other9.156
r_dihedral_angle_1_deg5.444
r_mcangle_it1.486
r_mcangle_other1.486
r_scangle_other1.42
r_angle_refined_deg1.1
r_scbond_it0.844
r_scbond_other0.844
r_mcbond_it0.835
r_mcbond_other0.835
r_angle_other_deg0.74
r_chiral_restr0.068
r_bond_refined_d0.006
r_bond_other_d0.005
r_gen_planes_refined0.004
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4982
Nucleic Acid Atoms
Solvent Atoms654
Heterogen Atoms

Software

Software
Software NamePurpose
HKL-2000data collection
CCP4model building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing