7FRK | pdb_00007frk

PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with Z30820160

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	0.1 M HEPES, 0.3 M magnesium acetate, 13.5% PEG 8000, 2% ethanol, and 1 mM BME

Crystal Properties
Matthews coefficient	Solvent content
3.3	62.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.586	α = 90
b = 89.586	β = 90
c = 106.334	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	277	PIXEL	DECTRIS PILATUS 6M		2019-07-17		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.96874	Diamond	I24

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.8	62.67	99.94	0.119	0.127	0.996	11.4			46252

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)	Redundancy	Number Unique Reflections (All)
1	1.8	1.83	99.91		2.584	2.795	0.321	0.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.8	62.67	44357	1816	99.83	0.1595	0.1583	0.19	0.1892	0.22	RANDOM	39.846

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]
0.01			0.01		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.611
r_dihedral_angle_4_deg	19.325
r_dihedral_angle_3_deg	15.159
r_dihedral_angle_1_deg	6.184
r_mcangle_it	4.68
r_mcbond_it	3.459
r_mcbond_other	3.401
r_angle_refined_deg	1.649
r_angle_other_deg	1.415
r_chiral_restr	0.088

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.611
r_dihedral_angle_4_deg	19.325
r_dihedral_angle_3_deg	15.159
r_dihedral_angle_1_deg	6.184
r_mcangle_it	4.68
r_mcbond_it	3.459
r_mcbond_other	3.401
r_angle_refined_deg	1.649
r_angle_other_deg	1.415
r_chiral_restr	0.088
r_bond_refined_d	0.017
r_gen_planes_refined	0.01
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2297
Nucleic Acid Atoms
Solvent Atoms	177
Heterogen Atoms	40

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2.multiplex	data scaling
DIALS	data reduction
DIMPLE	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.