2CFV | pdb_00002cfv

Crystal structure of human protein tyrosine phosphatase receptor type J

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP			0.01M NICL2,0.1M TRIS PH 8.5, 1M LI2SO4,150 UL SITTING DROPS

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.06	α = 90
b = 86.06	β = 90
c = 119.54	γ = 120

Symmetry
Space Group	H 3

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	MIRROS	2006-02-09	M	SINGLE WAVELENGTH

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

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	2.5	46.6	98.8	0.06	15.25	3.76		11491		3

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	2.5	2.6	91.2		0.27	4.18	3.13

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	PDB ENTRY 2AHS	2.5	63.25	10857	547	99.7	0.203	0.201	0.21	0.25	0.24	RANDOM	29.51

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]
1.23	0.62		1.23		-1.85

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.141
r_dihedral_angle_4_deg	18.465
r_dihedral_angle_3_deg	16.956
r_dihedral_angle_1_deg	6.914
r_scangle_it	1.683
r_angle_refined_deg	1.296
r_scbond_it	1.148
r_angle_other_deg	0.915
r_mcangle_it	0.846
r_mcbond_it	0.485
r_symmetry_vdw_refined	0.245
r_nbd_refined	0.229
r_nbd_other	0.197
r_nbtor_refined	0.19
r_symmetry_vdw_other	0.17
r_symmetry_hbond_refined	0.163
r_xyhbond_nbd_refined	0.155
r_nbtor_other	0.086
r_chiral_restr	0.072
r_bond_refined_d	0.012
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2130
Nucleic Acid Atoms
Solvent Atoms	25
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing