2QEP | pdb_00002qep

Crystal structure of the D1 domain of PTPRN2 (IA2beta)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2I1Y	PDB entry 2I1Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	0.2 M Na/KPO4, 0.1 M Bis-tris-propane pH 6.5, 20.0% PEG 3350, 10.0% Ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.541	α = 90
b = 136.555	β = 90
c = 35.752	γ = 90

Symmetry
Space Group	P 21 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		2007-05-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.99990	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	59.23	99.5	0.139	0.139	9.1	3.5	23096	23096

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.64	99.7		0.465	0.465	1.9	3.5	11455

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 2I1Y	2.5	59.23	21905	21905	1187	99.14	0.2389	0.2389	0.23634	0.24	0.28601	0.29	RANDOM	31.042

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]
1.7			-2.97		1.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.72
r_dihedral_angle_3_deg	15.183
r_dihedral_angle_4_deg	12.526
r_dihedral_angle_1_deg	6.512
r_scangle_it	1.556
r_angle_refined_deg	1.31
r_scbond_it	1.069
r_angle_other_deg	0.882
r_mcangle_it	0.789
r_mcbond_it	0.467
r_symmetry_vdw_other	0.291
r_symmetry_vdw_refined	0.264
r_nbd_refined	0.218
r_nbd_other	0.188
r_nbtor_refined	0.188
r_symmetry_hbond_refined	0.177
r_xyhbond_nbd_refined	0.15
r_mcbond_other	0.09
r_nbtor_other	0.086
r_chiral_restr	0.071
r_xyhbond_nbd_other	0.016
r_bond_refined_d	0.011
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	4413
Nucleic Acid Atoms
Solvent Atoms	39
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing