2FVV

Human Diphosphoinositol polyphosphate phosphohydrolase 1


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.527730% PEG8000, 0.2M Lithium sulphate, 0.1M SODIUM ACETATE, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.0439.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.653α = 90
b = 59.9β = 90
c = 61.735γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 135Helios Multilayer2005-12-27MSINGLE WAVELENGTH
21x-ray100CCDMARRESEARCHDouble crystal monochromator2005-12-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.5418
2SYNCHROTRONMAX II BEAMLINE I911-50.97957MAX III911-5

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
1,21.2527.4490.50.080923.938.885065545852-3
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)
1.251.3458.10.27572.741.55

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADFREE R1.2510506554585292290.50.1730.1710.1710.222RANDOM25.492
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
s_approx_iso_adps0.122
s_non_zero_chiral_vol0.109
s_similar_adp_cmpnt0.071
s_zero_chiral_vol0.068
s_angle_d0.037
s_from_restr_planes0.031
s_bond_d0.017
s_rigid_bond_adp_cmpnt0.006
s_similar_dist
s_anti_bump_dis_restr
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1181
Nucleic Acid Atoms
Solvent Atoms192
Heterogen Atoms42

Software

Software
Software NamePurpose
SHELXrefinement
PDB_EXTRACTdata extraction
PROTEUM PLUSdata reduction
SAINTdata reduction
XDSdata reduction
SADABSdata scaling
XSCALEdata scaling
SHELXDphasing
SHELXL-97refinement