7KEN

Protein Tyrosine Phosphatase 1B, D289A mutant, apo state

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6B90	PDB entry 6B90

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	277	100 mM HEPES, 200 mM magnesium acetate, 14% PEG8000

Crystal Properties
Matthews coefficient	Solvent content
3.17	61.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.314	α = 90
b = 88.314	β = 90
c = 104.155	γ = 120

Symmetry
Space Group	P 31 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS3 S 6M		2020-07-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.97741	ALS	5.0.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.8	76.48	100	0.178	0.187	0.056	0.997	6.2	10.8		40989			23.27

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.83	100		0.315	0.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 6B90	1.8	76.48	40989	2139	98.03	0.20561	0.20351	0.24369	RANDOM	38.766

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]
0.23	0.12		0.23		-0.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.349
r_dihedral_angle_4_deg	15.843
r_dihedral_angle_3_deg	15.198
r_long_range_B_other	11.235
r_long_range_B_refined	11.207
r_scangle_other	9.034
r_mcangle_it	7.273
r_mcangle_other	7.272
r_scbond_it	6.579
r_scbond_other	6.576
r_dihedral_angle_1_deg	6.31
r_mcbond_it	5.401
r_mcbond_other	5.38
r_angle_refined_deg	1.418
r_angle_other_deg	1.139
r_chiral_restr	0.087
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2431
Nucleic Acid Atoms
Solvent Atoms	187
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHENIX	phasing