7FQV | pdb_00007fqv

PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with XST00000847b

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
3.31	62.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.63	α = 90
b = 89.63	β = 90
c = 106.47	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	278	PIXEL	DECTRIS PILATUS 6M		2017-06-26		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97625	Diamond	I03

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	2.04	62.72	97.9	0.131	0.15	0.994	6.2			31334		-3	40.763

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	2.04	2.09	97.3		0.954	1.091	0.52	1.01

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	2.04	43.94	30103	1231	97.9	0.1886	0.1873	0.22	0.2227	0.25	RANDOM	41.585

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		0.01		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.863
r_dihedral_angle_4_deg	20.105
r_dihedral_angle_3_deg	15.234
r_dihedral_angle_1_deg	6.473
r_mcangle_it	4.556
r_mcbond_it	3.2
r_mcbond_other	3.17
r_angle_refined_deg	1.547
r_angle_other_deg	1.328
r_chiral_restr	0.073

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.863
r_dihedral_angle_4_deg	20.105
r_dihedral_angle_3_deg	15.234
r_dihedral_angle_1_deg	6.473
r_mcangle_it	4.556
r_mcbond_it	3.2
r_mcbond_other	3.17
r_angle_refined_deg	1.547
r_angle_other_deg	1.328
r_chiral_restr	0.073
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_bond_other_d	0.004
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2297
Nucleic Acid Atoms
Solvent Atoms	178
Heterogen Atoms	40

Software

Software
Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	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.