2Q9P

Human diphosphoinositol polyphosphate phosphohydrolase 1, Mg-F complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2FVVPDB entry 2FVV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.527730% PEG 8000, 200 mM LiCl, 5 mM MgCl2, 20 mM NaF, 5 mM IP6, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
1.935.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.193α = 90
b = 59.444β = 90
c = 62.547γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 135Helios multilayer mirrors2007-05-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR

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
11.655099.80.05411.72.12089020848-3
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)
1.651.7599.30.4612.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB entry 2FVV1.6532.212084820813106799.70.1940.1940.1920.23RANDOM15.789
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]
0.02-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.112
r_dihedral_angle_4_deg20.631
r_dihedral_angle_3_deg13.81
r_dihedral_angle_1_deg6.861
r_scangle_it4.469
r_scbond_it3.211
r_angle_refined_deg1.846
r_mcangle_it1.761
r_mcbond_it1.591
r_angle_other_deg1.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.112
r_dihedral_angle_4_deg20.631
r_dihedral_angle_3_deg13.81
r_dihedral_angle_1_deg6.861
r_scangle_it4.469
r_scbond_it3.211
r_angle_refined_deg1.846
r_mcangle_it1.761
r_mcbond_it1.591
r_angle_other_deg1.001
r_mcbond_other0.357
r_nbd_other0.215
r_nbd_refined0.212
r_metal_ion_refined0.188
r_xyhbond_nbd_refined0.183
r_symmetry_vdw_other0.18
r_nbtor_refined0.173
r_symmetry_hbond_refined0.157
r_chiral_restr0.122
r_nbtor_other0.094
r_symmetry_vdw_refined0.084
r_xyhbond_nbd_other0.027
r_bond_refined_d0.02
r_gen_planes_refined0.008
r_gen_planes_other0.003
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1110
Nucleic Acid Atoms
Solvent Atoms146
Heterogen Atoms87

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
PROTEUM PLUSdata collection
SAINTdata reduction
SADABSdata scaling
REFMACphasing