6WRY

CRYSTAL STRUCTURE OF INOSITOL POLYPHOSPHATE 1-PHOSPHATASE INPP1 IN COMPLEX GADOLINIUM AFTER ADDITION OF INOSITOL 1,3,4-TRISPHOSPHATE AT 2.5 ANGSTROM RESOLUTION


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.25293-Mg2+/-Li+/+Ins(1,3,4)P3/+Gd3+ (data=ip1r): Reservoir solution consisted of 10% PEG 8000, 80mM Bis-Tris, pH 5.25, 2mM Gd2(SO4)3, 1mM Ins(1,3,4)P3
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 II1994-07-22MSINGLE 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
12.86.95790.0614.21.515787
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)
12.83.02700.127

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 SYNTHESISTHROUGHOUT1INP2.86.95729143183.370.207420.204820.25027RANDOM20.325
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]
0.660.66-1.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.321
r_dihedral_angle_3_deg13.403
r_dihedral_angle_4_deg8.55
r_dihedral_angle_1_deg6.095
r_long_range_B_refined3.132
r_long_range_B_other3.104
r_mcangle_it1.659
r_mcangle_other1.659
r_scangle_other1.207
r_angle_refined_deg1.041
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.321
r_dihedral_angle_3_deg13.403
r_dihedral_angle_4_deg8.55
r_dihedral_angle_1_deg6.095
r_long_range_B_refined3.132
r_long_range_B_other3.104
r_mcangle_it1.659
r_mcangle_other1.659
r_scangle_other1.207
r_angle_refined_deg1.041
r_angle_other_deg0.993
r_mcbond_it0.909
r_mcbond_other0.907
r_scbond_other0.662
r_scbond_it0.661
r_chiral_restr0.027
r_bond_refined_d0.008
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 Atoms2521
Nucleic Acid Atoms
Solvent Atoms40
Heterogen Atoms14

Software

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