4O7I

Structural and functional characterization of 3'(2'),5'-bisphosphate nucleotidase1 from Entamoeba histolytica


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.528928% PEG 4000, 200mM lithium acetate, 5mM magnesium chloride, 5mM adenosine monophospahte, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.0640.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.445α = 90
b = 64.52β = 90
c = 117.184γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2011-08-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.54

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
12.15095.50.1313.78.21718316255-3
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)
12.12.1893.60.473.76.31648

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1QGX2.1150162541537587995.130.18670.184340.23167RANDOM24.42
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]
-1.87-0.021.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.781
r_dihedral_angle_3_deg11.864
r_dihedral_angle_4_deg10.004
r_long_range_B_other7.161
r_long_range_B_refined7.158
r_dihedral_angle_1_deg6.318
r_scangle_other6.268
r_scbond_it5.093
r_scbond_other5.092
r_mcangle_other3.227
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.781
r_dihedral_angle_3_deg11.864
r_dihedral_angle_4_deg10.004
r_long_range_B_other7.161
r_long_range_B_refined7.158
r_dihedral_angle_1_deg6.318
r_scangle_other6.268
r_scbond_it5.093
r_scbond_other5.092
r_mcangle_other3.227
r_mcangle_it3.224
r_mcbond_it2.499
r_mcbond_other2.49
r_angle_refined_deg1.337
r_angle_other_deg0.752
r_chiral_restr0.071
r_bond_refined_d0.01
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2453
Nucleic Acid Atoms
Solvent Atoms109
Heterogen Atoms6

Software

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