6WRO

CRYSTAL STRUCTURE OF INOSITOL POLYPHOSPHATE 1-PHOSPHATASE INPP1 IN COMPLEX GADOLINIUM BUT NO LITHIUM AT 3 ANGSTROM RESOLUTION


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.2529310% PEG 8000, 80mM Bis-Tris, pH 5.25, 2mM Gd2(SO4)3
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 IIsupper1994-08-10MSINGLE 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
138.378.60.083.51.312719
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)
133.23700.159

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 SYNTHESISTHROUGHOUT1INP38.28651739699.680.195340.192840.2359RANDOM25.572
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]
0.580.58-1.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.659
r_dihedral_angle_3_deg12.87
r_dihedral_angle_4_deg12.594
r_dihedral_angle_1_deg4.018
r_angle_refined_deg0.817
r_nbtor_refined0.29
r_nbd_refined0.147
r_symmetry_vdw_refined0.143
r_symmetry_hbond_refined0.114
r_xyhbond_nbd_refined0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.659
r_dihedral_angle_3_deg12.87
r_dihedral_angle_4_deg12.594
r_dihedral_angle_1_deg4.018
r_angle_refined_deg0.817
r_nbtor_refined0.29
r_nbd_refined0.147
r_symmetry_vdw_refined0.143
r_symmetry_hbond_refined0.114
r_xyhbond_nbd_refined0.09
r_chiral_restr0.048
r_metal_ion_refined0.008
r_bond_refined_d0.006
r_gen_planes_refined0.002
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_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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