5MWM

INOSITOL 1,3,4,5,6-PENTAKISPHOSPHATE 2-KINASE FROM M. MUSCULUS IN COMPLEX WITH IP6


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5MW8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.5291Magnesium Chloride, Sodium Acetate, PEG 6000
Crystal Properties
Matthews coefficientSolvent content
2.3446.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.55α = 90
b = 71.637β = 111.66
c = 61.822γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2016-05-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.979260ALBAXALOC

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.657.4699.613.36.615186

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 REPLACEMENTTHROUGHOUT5MW82.657.461439370798.990.255230.253430.28954RANDOM68.549
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]
2.91-12.44-1.026.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.58
r_dihedral_angle_3_deg17.695
r_dihedral_angle_4_deg14.903
r_long_range_B_other7.271
r_long_range_B_refined7.248
r_dihedral_angle_1_deg6.29
r_mcangle_it4.449
r_mcangle_other4.448
r_scangle_other3.969
r_mcbond_it2.572
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.58
r_dihedral_angle_3_deg17.695
r_dihedral_angle_4_deg14.903
r_long_range_B_other7.271
r_long_range_B_refined7.248
r_dihedral_angle_1_deg6.29
r_mcangle_it4.449
r_mcangle_other4.448
r_scangle_other3.969
r_mcbond_it2.572
r_mcbond_other2.566
r_scbond_it2.162
r_scbond_other2.103
r_angle_refined_deg1.286
r_angle_other_deg0.926
r_chiral_restr0.07
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
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 Atoms3278
Nucleic Acid Atoms
Solvent Atoms26
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
Aimlessdata scaling
Cootmodel building