4CML

Crystal Structure of INPP5B in complex with Phosphatidylinositol 3,4- bisphosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3N9VPDB ENTRY 3N9V

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
171.1 M NA-MALONATE PH 7.0, 0.1 M HEPES PH 7.0, 0.5% JEFFAMINE ED-2001 PH 7.0, 2MM MGSO4, 2MM PTDINS-(3,4,5)-P3 (1,2-DIOCTANOYL)
Crystal Properties
Matthews coefficientSolvent content
5.5877.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 133.661α = 90
b = 133.661β = 90
c = 133.661γ = 90
Symmetry
Space GroupP 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMARRESEARCHMIRRORS2010-04-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-2MAX III911-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.329.8999.90.097.85.535595-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.421000.651.25.6

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3N9V2.328.533778178699.990.176280.175060.1993RANDOM27.567
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.824
r_dihedral_angle_4_deg17.679
r_dihedral_angle_3_deg13.001
r_dihedral_angle_1_deg6.342
r_scangle_it2.351
r_scbond_it1.422
r_angle_refined_deg1.243
r_mcangle_it0.861
r_angle_other_deg0.78
r_mcbond_it0.436
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.824
r_dihedral_angle_4_deg17.679
r_dihedral_angle_3_deg13.001
r_dihedral_angle_1_deg6.342
r_scangle_it2.351
r_scbond_it1.422
r_angle_refined_deg1.243
r_mcangle_it0.861
r_angle_other_deg0.78
r_mcbond_it0.436
r_mcbond_other0.09
r_chiral_restr0.076
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_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 Atoms2496
Nucleic Acid Atoms
Solvent Atoms320
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing