8G67 | pdb_00008g67

Wildtype PTP1b in complex with DES4884

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		in-house structure of same protein

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.2	278	Reservoir solution: 50 mM MES (pH 6.2), 14% PEG6000, 50 mM MgCl2; Protein solution: 10.3 mg/ml PTP-1B 1-298 in 25 mM Hepes pH 7.2, 150 mM NaCl, 1 mM EDTA, 2 mM DTT

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.57	α = 90
b = 89.57	β = 90
c = 164.31	γ = 90

Symmetry
Space Group	P 43 21 2

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 PILATUS 6M		2016-08-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.92819	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.53	43.21	99.6	0.079	0.024	0.999	16.7	12		100903

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.53	1.57	99.9		1.945	0.694	0.55	1.1	8.8

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	in-house structure of same protein	1.53	43.21	95742	5035	99.58	0.15793	0.1544	0.16	0.22259	0.22	RANDOM	33.014

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]
1.29			1.29		-2.58

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	62.009
r_dihedral_angle_2_deg	35.291
r_sphericity_bonded	28.448
r_dihedral_angle_4_deg	17.447
r_dihedral_angle_3_deg	13.729
r_long_range_B_refined	10.523
r_long_range_B_other	10.522
r_scangle_other	9.97
r_scbond_it	8.782
r_scbond_other	8.782
r_mcangle_it	6.869
r_mcangle_other	6.869
r_dihedral_angle_1_deg	6.251
r_mcbond_it	5.639
r_mcbond_other	5.638
r_rigid_bond_restr	5.521
r_angle_refined_deg	1.855
r_angle_other_deg	1.033
r_chiral_restr	0.125
r_bond_refined_d	0.019
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001
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_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4632
Nucleic Acid Atoms
Solvent Atoms	540
Heterogen Atoms	47

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing