4QXD

Crystal structure of Inositol Polyphosphate 1-Phosphatase from Entamoeba histolytica


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.728912.5% MPD, 12.5% Peg 1k, 12.5% Peg 3350, 0.03M salt mixture, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.1141.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.741α = 90
b = 76.289β = 90
c = 101.067γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2012-04-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.54170

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
12.555099.90.124.2912.119012-3
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)
12.552.6499.80.54.3211.61876

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 REPLACEMENTTHROUGHOUTModel obtained from low resolution anomalous data2.55501798997599.780.195730.192910.24954RANDOM50.583
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]
2.02-2.920.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.089
r_dihedral_angle_3_deg14.391
r_dihedral_angle_4_deg6.312
r_dihedral_angle_1_deg6.209
r_long_range_B_refined4.708
r_long_range_B_other4.704
r_scangle_other3.273
r_mcangle_it2.509
r_mcangle_other2.509
r_scbond_it2.052
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.089
r_dihedral_angle_3_deg14.391
r_dihedral_angle_4_deg6.312
r_dihedral_angle_1_deg6.209
r_long_range_B_refined4.708
r_long_range_B_other4.704
r_scangle_other3.273
r_mcangle_it2.509
r_mcangle_other2.509
r_scbond_it2.052
r_scbond_other2.037
r_mcbond_it1.57
r_mcbond_other1.57
r_angle_refined_deg1.187
r_angle_other_deg0.828
r_chiral_restr0.063
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_bond_other_d0.003
r_gen_planes_other0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4566
Nucleic Acid Atoms
Solvent Atoms28
Heterogen Atoms16

Software

Software
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling