6X25

CRYSTAL STRUCTURE OF INOSITOL POLYPHOSPHATE 1-PHOSPHATASE INPP1 IN COMPLEX GADOLINIUM AFTER ADDITION OF INOSITOL 1,3,4-TRISPHOSPHATE AND LITHIUM AT 3.2 ANGSTROM RESOLUTION


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1INP 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.25293Tetragonal shaped crystals amenable to diffraction studies were grown by the hanging drop vapor diffusion method on silanized glass covers slips at 20 C and grew with dimensions routinely exceeding 0.1 x 0.1 x 0.5mm. Gd3+, a competitive inhibitor of Mg2+, has a useful anomalous absorption edge at the CuK wavelength and therefore was used in the co-crystallization or soaking conditions. -Mg2+/+Li+/+Ins(1,3,4)P3/+Gd3+ (data=ip7r): Reservoir solution consisted of 10% PEG 8000, 80mM Bis-Tris, pH 5.25, 2mM Gd2(SO4)3, 1mM Ins(1,3,4)P3; 200mM Li2SO4
Crystal Properties
Matthews coefficientSolvent content
2.1743.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.64α = 90
b = 51.64β = 90
c = 143.33γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray296AREA DETECTORUCSD MARK II1994-08-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.542

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
13.210.22850.1033.82.111374
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)
13.23.450.193

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 SYNTHESISTHROUGHOUT1INP3.210.22552734094.610.201610.198830.24551RANDOM34.415
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]
0.760.76-1.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.071
r_dihedral_angle_3_deg12.952
r_dihedral_angle_4_deg9.438
r_dihedral_angle_1_deg6.124
r_long_range_B_refined3.661
r_long_range_B_other3.388
r_mcangle_it1.041
r_mcangle_other1.041
r_angle_refined_deg1.04
r_angle_other_deg0.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.071
r_dihedral_angle_3_deg12.952
r_dihedral_angle_4_deg9.438
r_dihedral_angle_1_deg6.124
r_long_range_B_refined3.661
r_long_range_B_other3.388
r_mcangle_it1.041
r_mcangle_other1.041
r_angle_refined_deg1.04
r_angle_other_deg0.99
r_mcbond_it0.547
r_mcbond_other0.547
r_scangle_other0.471
r_scbond_it0.221
r_scbond_other0.198
r_chiral_restr0.026
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_bond_other_d0.004
r_gen_planes_other0.004
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 Atoms2536
Nucleic Acid Atoms
Solvent Atoms16
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
UCSD-systemdata reduction
UCSD-systemdata scaling
SQUASHphasing