3ZK4

Structure of purple acid phosphatase PPD1 isolated from yellow lupin (Lupinus luteus) seeds


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.50.12 M ALCOHOLS, 0.1 M BUFFER SYSTEM (1M MES AND 1M IMIDAZOLE) AT PH 6.5, AND 30% PRECIPITANT (COMPRISING 40% GLYCEROL AND 20% PEG4000)
Crystal Properties
Matthews coefficientSolvent content
3.3763.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 223.925α = 90
b = 223.925β = 90
c = 111.904γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMIRRORS2012-06-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 1SOLEILPROXIMA 1

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
11.655098.60.09206.733210018.6
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)
11.651.7199.80.726.6

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 DIFFRACTIONSADTHROUGHOUTNONE1.6541.623146541676098.40.150850.149590.17459RANDOM21.923
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]
0.420.42-0.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.796
r_dihedral_angle_4_deg12.505
r_dihedral_angle_3_deg12.257
r_dihedral_angle_1_deg6.945
r_angle_refined_deg1.68
r_angle_other_deg0.827
r_chiral_restr0.133
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.796
r_dihedral_angle_4_deg12.505
r_dihedral_angle_3_deg12.257
r_dihedral_angle_1_deg6.945
r_angle_refined_deg1.68
r_angle_other_deg0.827
r_chiral_restr0.133
r_bond_refined_d0.014
r_gen_planes_refined0.008
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13636
Nucleic Acid Atoms
Solvent Atoms2543
Heterogen Atoms387

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing