7FRU

PanDDA analysis group deposition of ground-state model of PTP1B, using pre-clustering, cluster 2


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
3.2962.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.541α = 90
b = 89.541β = 90
c = 106.301γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray277PIXELDECTRIS PILATUS 6M2019-07-03SINGLE 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
11.9853.1595.210.120.1410.9116.733204
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)
11.982.0192.611.3841.6150.3290.7

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 REPLACEMENTTHROUGHOUT1.9844.8131425129393.870.16770.16590.2128RANDOM46.455
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]
0.210.110.21-0.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.94
r_dihedral_angle_4_deg21.149
r_dihedral_angle_3_deg14.448
r_dihedral_angle_1_deg6.712
r_mcangle_it5.19
r_mcbond_it3.73
r_mcbond_other3.655
r_angle_refined_deg1.544
r_angle_other_deg1.36
r_chiral_restr0.074
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.94
r_dihedral_angle_4_deg21.149
r_dihedral_angle_3_deg14.448
r_dihedral_angle_1_deg6.712
r_mcangle_it5.19
r_mcbond_it3.73
r_mcbond_other3.655
r_angle_refined_deg1.544
r_angle_other_deg1.36
r_chiral_restr0.074
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.004
r_gen_planes_other0.002
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