2OC3 | pdb_00002oc3

Crystal Structure of the Catalytic Domain of Human Protein Tyrosine Phosphatase non-receptor Type 18

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2B49	pdb entries 2B49, 1GWZ
experimental model	PDB	1GWZ	pdb entries 2B49, 1GWZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.8	277	0.1M HEPES, 25% PEG-3350, 6% Jeffamine M-600, pH 6.8, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.338	α = 90
b = 63.763	β = 102.64
c = 48.992	γ = 90

Symmetry
Space Group	P 1 21 1

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		2006-11-26	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)	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	1.5	38.24	99.3	0.065	0.065	12.4	3.7		44277			13.7

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)
	1.5	1.58	95.2		0.343	0.343	3.4	3.1	19366

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 entries 2B49, 1GWZ	1.5	38.24	42028	42028	2228	99.25	0.15557	0.15557	0.15407	0.162	0.18395	0.1858	RANDOM	11.822

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]
-0.11		0.24	-0.3		0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.923
r_dihedral_angle_4_deg	17.219
r_dihedral_angle_3_deg	11.71
r_scangle_it	6.543
r_dihedral_angle_1_deg	5.659
r_scbond_it	5.071
r_mcangle_it	4.052
r_mcbond_it	3.364
r_angle_refined_deg	1.471
r_mcbond_other	1.08
r_angle_other_deg	0.93
r_symmetry_vdw_other	0.293
r_nbd_refined	0.216
r_nbd_other	0.204
r_nbtor_refined	0.181
r_symmetry_hbond_refined	0.179
r_xyhbond_nbd_refined	0.145
r_symmetry_vdw_refined	0.127
r_chiral_restr	0.09
r_nbtor_other	0.085
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2228
Nucleic Acid Atoms
Solvent Atoms	277
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
MOSFLM	data reduction
CCP4	data scaling
PHASER	phasing