7E4L

Conversion of pyrophosphate-dependent myo-inositol-1 kinase into myo-inositol-3 kinase by N78L/S89L mutation


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5YSP 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION29326% (w/v) poly(ethylene glycol) 4000, 2mM ammonium sulfate, 100mM sodium acetate buffer (pH 5.4)
Crystal Properties
Matthews coefficientSolvent content
2.0339.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.205α = 83.53
b = 46.398β = 80.43
c = 66.544γ = 68.57
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95PIXELDECTRIS PILATUS 2M2019-11-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NE3A1Photon FactoryAR-NE3A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)CC (Half)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
11.65062.50.0510.99719.83.443707
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6494.60.1340.9859.13.58

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT5ysp1.642.6541534217365.360.193010.191790.21555RANDOM15.558
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]
-0.270.210.15-0.330.320.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.024
r_dihedral_angle_4_deg11.99
r_dihedral_angle_3_deg11.658
r_dihedral_angle_1_deg6.864
r_long_range_B_refined3.233
r_long_range_B_other3.218
r_angle_other_deg2.307
r_scangle_other1.689
r_mcangle_it1.513
r_mcangle_other1.513
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.024
r_dihedral_angle_4_deg11.99
r_dihedral_angle_3_deg11.658
r_dihedral_angle_1_deg6.864
r_long_range_B_refined3.233
r_long_range_B_other3.218
r_angle_other_deg2.307
r_scangle_other1.689
r_mcangle_it1.513
r_mcangle_other1.513
r_angle_refined_deg1.304
r_scbond_other1.048
r_scbond_it1.047
r_mcbond_it0.894
r_mcbond_other0.893
r_chiral_restr0.057
r_bond_other_d0.036
r_gen_planes_other0.007
r_bond_refined_d0.005
r_gen_planes_refined0.005
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 Atoms4266
Nucleic Acid Atoms
Solvent Atoms193
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing