2NLK | pdb_00002nlk

Crystal structure of D1 and D2 catalytic domains of human Protein Tyrosine Phosphatase Gamma (D1+D2 PTPRG)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2H4V	PDB ENTRies 2H4V, 2C7S, 1RPM, 1YF0, 1H02, 1GWZ
experimental model	PDB	2C7S	PDB ENTRies 2H4V, 2C7S, 1RPM, 1YF0, 1H02, 1GWZ
experimental model	PDB	1RPM	PDB ENTRies 2H4V, 2C7S, 1RPM, 1YF0, 1H02, 1GWZ
experimental model	PDB	1YF0	PDB ENTRies 2H4V, 2C7S, 1RPM, 1YF0, 1H02, 1GWZ
experimental model	PDB	1H02	PDB ENTRies 2H4V, 2C7S, 1RPM, 1YF0, 1H02, 1GWZ
experimental model	PDB	1GWZ	PDB ENTRies 2H4V, 2C7S, 1RPM, 1YF0, 1H02, 1GWZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	277	10% PEG 10K, 100mM Imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.27	62.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.51	α = 90
b = 133.996	β = 90
c = 59.084	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	IMAGE PLATE	RIGAKU RAXIS		2006-09-19	M	SINGLE WAVELENGTH
2	1

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

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	2.4	39.936	99.5	0.099	0.099	5.9	4.2	37606	37418

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	2.4	2.53	98.6		0.485	0.485	1.5	3.6	5313

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 2H4V, 2C7S, 1RPM, 1YF0, 1H02, 1GWZ	2.4	39.936	37639	37345	1864	99.22	0.239	0.239	0.237	0.23	0.274	0.27	RANDOM	22.159

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]
1.32			-0.78		-0.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.546
r_dihedral_angle_4_deg	20.899
r_dihedral_angle_3_deg	14.692
r_dihedral_angle_1_deg	7.626
r_scangle_it	2.469
r_scbond_it	1.651
r_angle_refined_deg	1.565
r_mcangle_it	1.066
r_angle_other_deg	1.06
r_mcbond_it	0.641
r_symmetry_vdw_other	0.196
r_nbd_refined	0.195
r_nbd_other	0.193
r_nbtor_refined	0.176
r_xyhbond_nbd_refined	0.16
r_chiral_restr	0.133
r_mcbond_other	0.132
r_symmetry_vdw_refined	0.123
r_symmetry_hbond_refined	0.103
r_nbtor_other	0.087
r_bond_refined_d	0.015
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4386
Nucleic Acid Atoms
Solvent Atoms	150
Heterogen Atoms

Software

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