4PBX

Crystal structure of the six N-terminal domains of human receptor protein tyrosine phosphatase sigma

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2YD3	2YD3, 2YD4, 2YD9, 2DJU
experimental model	PDB	2YD4	2YD3, 2YD4, 2YD9, 2DJU
experimental model	PDB	2YD9	2YD3, 2YD4, 2YD9, 2DJU
experimental model	PDB	2DJU	2YD3, 2YD4, 2YD9, 2DJU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293.5	10 % PEG 400, 0.01 M magnesium chloride, 0.1 M potassium chloride, 0.05 M MES pH 6.0

Crystal Properties
Matthews coefficient	Solvent content
5.87	79.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 198.78	α = 90
b = 198.78	β = 90
c = 132.4	γ = 120

Symmetry
Space Group	P 61 2 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	ADSC QUANTUM 315r		2008-09-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.9788	ESRF	ID29

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	3.15	99.4	95.6	0.078	17.8	7.6		25619

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	3.15	3.23	96.1		0.991	2.1	7.5

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	2YD3, 2YD4, 2YD9, 2DJU	3.15	172.15	24310	1309	94.29	0.23562	0.23406	0.24	0.26497	0.26	RANDOM	120.828

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]
0.7	0.35		0.7		-2.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.678
r_dihedral_angle_3_deg	14.843
r_dihedral_angle_4_deg	14.675
r_dihedral_angle_1_deg	5.945
r_long_range_B_refined	4.515
r_long_range_B_other	4.515
r_mcangle_it	2.909
r_mcangle_other	2.909
r_scangle_other	2.525
r_mcbond_other	1.658
r_mcbond_it	1.657
r_scbond_it	1.395
r_scbond_other	1.395
r_angle_refined_deg	1.008
r_angle_other_deg	0.667
r_chiral_restr	0.06
r_bond_refined_d	0.005
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4380
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	28

Software

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