2H04 | pdb_00002h04

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 (WITH MODIFICATIONS)

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
1.96	37.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.803	α = 90
b = 70.12	β = 90
c = 90.722	γ = 90

Symmetry
Space Group	P 21 21 21

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	ADSC QUANTUM 4		2005-03-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.0	APS	17-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	2.3	34.86	99.6	0.09	8.88	3.8	13248	13248			22

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)
	2.3	2.4	98.3		0.37	2.83	3.1	1529

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 (WITH MODIFICATIONS)	2.3	34.86	13207	13207	649	99.65	0.172	0.17	0.169	0.17	0.238	0.24	RANDOM	16.455

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]
0.12			-0.23		0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.525
r_dihedral_angle_3_deg	19.278
r_dihedral_angle_4_deg	18.391
r_dihedral_angle_1_deg	8.347
r_scangle_it	6.463
r_scbond_it	4.613
r_mcangle_it	2.793
r_angle_refined_deg	2.155
r_mcbond_it	1.702
r_symmetry_hbond_refined	0.329

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.525
r_dihedral_angle_3_deg	19.278
r_dihedral_angle_4_deg	18.391
r_dihedral_angle_1_deg	8.347
r_scangle_it	6.463
r_scbond_it	4.613
r_mcangle_it	2.793
r_angle_refined_deg	2.155
r_mcbond_it	1.702
r_symmetry_hbond_refined	0.329
r_nbtor_refined	0.319
r_symmetry_vdw_refined	0.257
r_nbd_refined	0.222
r_xyhbond_nbd_refined	0.193
r_chiral_restr	0.145
r_bond_refined_d	0.009
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2300
Nucleic Acid Atoms
Solvent Atoms	141
Heterogen Atoms	32

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.