2IXM

Structure of human PTPA


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293PTPA CRYSTALS WERE GROWN USING THE HANGING DROP METHOD AT 20C. 1UL OF PROTEIN (20 MG/ML) WAS MIXED WITH 1 UL OF PRECIPITANT (23% TO 28% PEG 4000, 0.2 M LITHIUM SULFATE, 0.1 M TRIS PH 7.0-8.5 AND 5 MM DTT) WERE EQUILIBRATED AGAINST 0.5 ML OF PRECIPITANT. LARGE PLATE CRYSTALS APPEARED IN 2 TO 3 DAYS. FOR CRYOPROTECTION 5% MPD WAS ADDED TO THE PRECIPITANT SOLUTION.
Crystal Properties
Matthews coefficientSolvent content
2.1639.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.243α = 90
b = 70.41β = 90
c = 95.534γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2005-05-09MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
11.52299.90.0913.75.9311889
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)
11.51.581000.35.95.9

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 DIFFRACTIONMADTHROUGHOUT1.556.750109269099.90.2030.2020.221RANDOM12.59
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]
-0.46-0.120.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.773
r_dihedral_angle_4_deg16.514
r_dihedral_angle_3_deg11.149
r_dihedral_angle_1_deg5.052
r_scangle_it2.924
r_scbond_it1.868
r_angle_refined_deg1.207
r_mcangle_it1.12
r_mcbond_it0.703
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.773
r_dihedral_angle_4_deg16.514
r_dihedral_angle_3_deg11.149
r_dihedral_angle_1_deg5.052
r_scangle_it2.924
r_scbond_it1.868
r_angle_refined_deg1.207
r_mcangle_it1.12
r_mcbond_it0.703
r_nbtor_refined0.306
r_nbd_refined0.205
r_symmetry_vdw_refined0.165
r_xyhbond_nbd_refined0.113
r_chiral_restr0.083
r_symmetry_hbond_refined0.077
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
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 Atoms2431
Nucleic Acid Atoms
Solvent Atoms242
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing