7FRT

PanDDA analysis group deposition of ground-state model of PTP1B, using pre-clustering, cluster 1


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52930.1 M HEPES, 0.3 M magnesium acetate, 13.5% PEG 8000, 2% ethanol, and 1 mM BME
Crystal Properties
Matthews coefficientSolvent content
3.362.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.565α = 90
b = 89.565β = 90
c = 106.356γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray277PIXELDECTRIS PILATUS 6M2019-07-17SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.96874DiamondI24

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)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
11.8653.1899.860.1310.1440.99941901
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.861.891001.8772.0820.3130.7

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.8644.8240179164499.720.16090.15970.1902RANDOM39.475
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]
0.10.050.1-0.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.457
r_dihedral_angle_4_deg21.502
r_dihedral_angle_3_deg14.91
r_dihedral_angle_1_deg6.537
r_mcangle_it4.978
r_mcbond_it3.683
r_mcbond_other3.619
r_angle_refined_deg1.65
r_angle_other_deg1.439
r_chiral_restr0.082
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.457
r_dihedral_angle_4_deg21.502
r_dihedral_angle_3_deg14.91
r_dihedral_angle_1_deg6.537
r_mcangle_it4.978
r_mcbond_it3.683
r_mcbond_other3.619
r_angle_refined_deg1.65
r_angle_other_deg1.439
r_chiral_restr0.082
r_bond_refined_d0.013
r_gen_planes_refined0.01
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2297
Nucleic Acid Atoms
Solvent Atoms180
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
xia2.multiplexdata scaling
DIALSdata reduction
DIMPLEphasing