2H03 | pdb_00002h03

Structural studies of protein tyrosine phosphatase beta catalytic domain in complex with inhibitors

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RPM	PDB ENTRY 1RPM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8	298	21% PEG 8000, 220 mM MgCl2, 1% BME, 0.1% BOG, 5mM DTT, pH 8.0, vapor diffusion, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 112.316	α = 90
b = 38.934	β = 103.91
c = 66.062	γ = 90

Symmetry
Space Group	C 1 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	CCD	MARRESEARCH		2006-02-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.65	27.6	97.7	0.028	19.89	2.8	32934	32934			23

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.75	91.1		0.254	3.89	2.2	4904

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	PDB ENTRY 1RPM	1.65	27.6	32933	32933	1681	97.7	0.182	0.18	0.18	0.19	0.217	0.23	RANDOM	24.4

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]
-0.04		-0.79	0.25		-0.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.72
r_dihedral_angle_4_deg	13.48
r_dihedral_angle_3_deg	13.313
r_dihedral_angle_1_deg	7.031
r_scangle_it	6.012
r_scbond_it	4.051
r_mcangle_it	2.591
r_angle_refined_deg	1.717
r_mcbond_it	1.684
r_nbtor_refined	0.321

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.72
r_dihedral_angle_4_deg	13.48
r_dihedral_angle_3_deg	13.313
r_dihedral_angle_1_deg	7.031
r_scangle_it	6.012
r_scbond_it	4.051
r_mcangle_it	2.591
r_angle_refined_deg	1.717
r_mcbond_it	1.684
r_nbtor_refined	0.321
r_symmetry_vdw_refined	0.258
r_nbd_refined	0.228
r_xyhbond_nbd_refined	0.226
r_symmetry_hbond_refined	0.217
r_chiral_restr	0.138
r_metal_ion_refined	0.022
r_bond_refined_d	0.012
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2350
Nucleic Acid Atoms
Solvent Atoms	202
Heterogen Atoms	37

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
HKL-2000	data scaling
AMoRE	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.