4RKK

Structure of a product bound phosphatase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5277250 mM maltohexaose, 0.19 M Sodium Acetate, 0.1 M Sodium Citrate, 25.5% PEG3350, 15% Glycerol, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
2VAPOR DIFFUSION, HANGING DROP5277250 mM maltohexaose, 0.17 M Sodium Acetate, 0.08 M Sodium Citrate, 25.5% PEG4000, 15% Glycerol, 30 mM Sodium Tungstate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.706α = 90
b = 78.706β = 90
c = 321.124γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2013-06-07MSINGLE WAVELENGTH
22x-rayMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0000, 1.2148APS22-ID
2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
1,22.42092.337585-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1,22.42.4992

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT2.419.9833896358291.970.170550.166340.21053RANDOM52.542
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]
-0.05-0.050.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.43
r_dihedral_angle_4_deg19.589
r_dihedral_angle_3_deg14.388
r_long_range_B_other9.316
r_long_range_B_refined9.311
r_scangle_other7.655
r_dihedral_angle_1_deg5.637
r_scbond_it5.235
r_scbond_other5.234
r_mcangle_it5.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.43
r_dihedral_angle_4_deg19.589
r_dihedral_angle_3_deg14.388
r_long_range_B_other9.316
r_long_range_B_refined9.311
r_scangle_other7.655
r_dihedral_angle_1_deg5.637
r_scbond_it5.235
r_scbond_other5.234
r_mcangle_it5.001
r_mcangle_other5
r_mcbond_other3.387
r_mcbond_it3.385
r_angle_refined_deg1.543
r_angle_other_deg0.952
r_chiral_restr0.145
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5022
Nucleic Acid Atoms
Solvent Atoms144
Heterogen Atoms345

Software

Software
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing