3S3F

Crystal Structure of the catalytic domain of PTP10D from Drosophila melanogaster with a small molecule inhibitor Vanadate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3S3EPDB ID 3S3E

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529315% PEG 4000, 120mM Citrate, 10% iso-propanol, 10% n-Butanol, 10% 1,4-Butanediol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.766.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.07α = 90
b = 103.07β = 90
c = 173.401γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDbent collimating mirror and toroid2010-11-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM141.00ESRFBM14

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
12.7451000.11311.95.829943-544.99
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)
12.72.851000.4353.75.825051

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ID 3S3E2.739.682835728357151499.80.239820.239820.238130.27177RANDOM38.07
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]
0.120.060.12-0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.811
r_dihedral_angle_4_deg18.134
r_dihedral_angle_3_deg17.82
r_dihedral_angle_1_deg6.885
r_scangle_it2.062
r_scbond_it1.264
r_angle_refined_deg1.261
r_mcangle_it0.711
r_mcbond_it0.357
r_chiral_restr0.101
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.811
r_dihedral_angle_4_deg18.134
r_dihedral_angle_3_deg17.82
r_dihedral_angle_1_deg6.885
r_scangle_it2.062
r_scbond_it1.264
r_angle_refined_deg1.261
r_mcangle_it0.711
r_mcbond_it0.357
r_chiral_restr0.101
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4684
Nucleic Acid Atoms
Solvent Atoms90
Heterogen Atoms29

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling