2OOQ | pdb_00002ooq

Crystal Structure of the Human Receptor Phosphatase PTPRT

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RPM	PDB entries 1RPM, 2C7S, 1LAR, 2FH7
experimental model	PDB	2C7S	PDB entries 1RPM, 2C7S, 1LAR, 2FH7
experimental model	PDB	1LAR	PDB entries 1RPM, 2C7S, 1LAR, 2FH7
experimental model	PDB	2FH7	PDB entries 1RPM, 2C7S, 1LAR, 2FH7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	0.2M LiCl, 0.1M HEPES, 20.0% PEG 6000, 10.0% Ethylene glycol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.186	α = 90
b = 86.697	β = 99.89
c = 91.12	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	IMAGE PLATE	RIGAKU RAXIS HTC		2007-01-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.54180

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	1.8	89.77	100	0.092	0.092	16	3.7		52802			18.6

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	1.8	1.9	100		0.595	0.595	2.6	3.6

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 (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 1RPM, 2C7S, 1LAR, 2FH7	1.8	89.77	50081	50081	2688	99.92	0.14709	0.14709	0.14488	0.16	0.18758	0.2	RANDOM	22.417

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]
0.09		-0.35	0.3		-0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.446
r_dihedral_angle_4_deg	18.286
r_dihedral_angle_3_deg	12.178
r_scangle_it	8.471
r_scbond_it	7.122
r_dihedral_angle_1_deg	6.4
r_mcangle_it	4.816
r_mcbond_it	3.651
r_mcbond_other	1.839
r_angle_refined_deg	1.453
r_angle_other_deg	0.909
r_symmetry_vdw_other	0.26
r_nbd_refined	0.217
r_nbd_other	0.202
r_nbtor_refined	0.182
r_symmetry_hbond_refined	0.174
r_xyhbond_nbd_refined	0.162
r_symmetry_vdw_refined	0.093
r_chiral_restr	0.089
r_nbtor_other	0.085
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4421
Nucleic Acid Atoms
Solvent Atoms	436
Heterogen Atoms	35

Software

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