3HQC | pdb_00003hqc

Crystal structure of Phosphotyrosine-binding domain from the Human Tensin-like C1 domain-containing phosphatase (TENC1)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1WVH	Poly-Alanine model of the PDB entry 1WVH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	294	100mM Sodium Acetate pH 4 + 2% Glycerol + 2000mM Ammonium Sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
3.58	65.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.909	α = 90
b = 108.909	β = 90
c = 36.196	γ = 120

Symmetry
Space Group	P 65

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	MAR CCD 165 mm		2009-02-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.9793	APS	31-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	47.14	100	0.118	8.3	10.9		23089			25.92

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.9	100		0.637	3	10.7	3337

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	Poly-Alanine model of the PDB entry 1WVH	1.8	26.16	23037	1182	100	0.214	0.212	0.23	0.242	0.25	RANDOM	33.104

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]
0.02	0.01		0.02		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.696
r_dihedral_angle_4_deg	15.098
r_dihedral_angle_3_deg	10.74
r_dihedral_angle_1_deg	5.917
r_scangle_it	3.216
r_scbond_it	2.126
r_mcangle_it	1.804
r_angle_refined_deg	1.382
r_mcbond_it	1.186
r_angle_other_deg	0.86
r_mcbond_other	0.244
r_symmetry_vdw_other	0.218
r_nbd_refined	0.2
r_nbd_other	0.199
r_nbtor_refined	0.175
r_symmetry_hbond_refined	0.153
r_xyhbond_nbd_refined	0.142
r_symmetry_vdw_refined	0.119
r_chiral_restr	0.087
r_nbtor_other	0.086
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1040
Nucleic Acid Atoms
Solvent Atoms	79
Heterogen Atoms	29

Software

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