2EJ8

Crystal structure of APPL1 PTB domain at 1.8A


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5277100mM Na Citrate, 10% PEG 3350, 15% Isopropanol, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.0439.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.23α = 90
b = 63.566β = 102.67
c = 52.449γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102006-12-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A0.97900Photon FactoryAR-NW12A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.845097.30.1040.1039.598013.565224816-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.841.9291.40.4550.3312.737832.51784

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.8450323949128099.790.195260.193320.23014RANDOM23.701
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]
-0.7-1.480.16-0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it6.408
r_dihedral_angle_1_deg5.684
r_scbond_it3.793
r_mcangle_it2.797
r_mcbond_it1.476
r_angle_refined_deg1.438
r_angle_other_deg0.805
r_nbd_refined0.364
r_symmetry_hbond_refined0.263
r_symmetry_vdw_other0.257
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it6.408
r_dihedral_angle_1_deg5.684
r_scbond_it3.793
r_mcangle_it2.797
r_mcbond_it1.476
r_angle_refined_deg1.438
r_angle_other_deg0.805
r_nbd_refined0.364
r_symmetry_hbond_refined0.263
r_symmetry_vdw_other0.257
r_nbd_other0.253
r_symmetry_vdw_refined0.174
r_xyhbond_nbd_refined0.165
r_chiral_restr0.094
r_nbtor_other0.082
r_bond_refined_d0.018
r_gen_planes_refined0.006
r_bond_other_d0.005
r_gen_planes_other0.003
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2105
Nucleic Acid Atoms
Solvent Atoms168
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing