6WRR

CRYSTAL STRUCTURE OF INOSITOL POLYPHOSPHATE 1-PHOSPHATASE INPP1 IN COMPLEX GADOLINIUM AND LITHIUM 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 DROP6.329313% PEG8000, 200mM Li2SO4 and 100mM Tris, pH 6.3. Upon reaching maximum size after ~5 days, a Gd3+ heavy atom derivative was prepared by adding 0.5uL of 17.5mM Gd2(SO4)3 in reservoir solution to 3uL hanging drops (2.5mM final Gd3+) containing native crystals for 48 hours
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 II1992-07-10MSINGLE 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
12.515.45960.05110.83.426197
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)
12.52.6995.60.172

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 SYNTHESISTHROUGHOUT1INP2.515.451164572599.980.165370.162860.20497RANDOM32.228
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]
0.780.78-1.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.225
r_dihedral_angle_3_deg15.766
r_dihedral_angle_4_deg13.114
r_dihedral_angle_1_deg5.254
r_scangle_it1.333
r_angle_refined_deg1.056
r_scbond_it0.819
r_mcangle_it0.748
r_mcbond_it0.432
r_nbtor_refined0.296
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.225
r_dihedral_angle_3_deg15.766
r_dihedral_angle_4_deg13.114
r_dihedral_angle_1_deg5.254
r_scangle_it1.333
r_angle_refined_deg1.056
r_scbond_it0.819
r_mcangle_it0.748
r_mcbond_it0.432
r_nbtor_refined0.296
r_symmetry_vdw_refined0.211
r_nbd_refined0.181
r_symmetry_hbond_refined0.138
r_xyhbond_nbd_refined0.116
r_chiral_restr0.069
r_metal_ion_refined0.01
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2532
Nucleic Acid Atoms
Solvent Atoms85
Heterogen Atoms12

Software

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