2I75 | pdb_00002i75

Crystal Structure of Human Protein Tyrosine Phosphatase N4 (PTPN4)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2B49

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.8	293	0.1M HEPES, 0.1 M NaCl, 1.3 M (NH4)SO4. , pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.075	α = 90
b = 66.075	β = 90
c = 144.508	γ = 90

Symmetry
Space Group	P 41 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	CCD	MARMOSAIC 225 mm CCD		2006-07-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.979	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.45	38.92	95.6			11901	11901

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.45	2.58	98.6

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 (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	2B49	2.45	38.92	11249	11249	582	95.38	0.22671	0.22359	0.23	0.29104	0.29	RANDOM	25.129

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]
2.22			2.22		-4.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.601
r_dihedral_angle_4_deg	16.13
r_dihedral_angle_3_deg	16.128
r_dihedral_angle_1_deg	6.622
r_scangle_it	1.693
r_angle_refined_deg	1.347
r_scbond_it	1.111
r_angle_other_deg	1.089
r_mcangle_it	0.724
r_mcbond_it	0.459
r_symmetry_vdw_refined	0.214
r_nbd_refined	0.211
r_symmetry_vdw_other	0.201
r_nbd_other	0.196
r_nbtor_refined	0.183
r_xyhbond_nbd_refined	0.158
r_chiral_restr	0.131
r_symmetry_hbond_refined	0.111
r_nbtor_other	0.087
r_mcbond_other	0.086
r_bond_refined_d	0.012
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2089
Nucleic Acid Atoms
Solvent Atoms	51
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
PHASER	phasing