2AHS | pdb_00002ahs

Crystal Structure of the Catalytic Domain of Human Tyrosine Receptor Phosphatase Beta

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RPM	1RPM.PDB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7	277	PEG6000, Ethylene Glycol, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 7.00

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.368	α = 90
b = 123.368	β = 90
c = 179.569	γ = 120

Symmetry
Space Group	P 61 2 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		2005-07-04	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)	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	2.1	53.4	99.2				47341

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.21	95.1

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 (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	1RPM.PDB	2.1	53.4	44882	44882	2394	99.2	0.155	0.152	0.2	0.206	0.2	RANDOM	23.14

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]
-0.19	-0.09		-0.19		0.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.211
r_dihedral_angle_3_deg	13.223
r_dihedral_angle_4_deg	13.063
r_scangle_it	11.135
r_scbond_it	9.518
r_mcangle_it	6.752
r_dihedral_angle_1_deg	6.312
r_mcbond_it	5.038
r_mcbond_other	2.003
r_angle_refined_deg	1.337
r_angle_other_deg	0.895
r_symmetry_hbond_refined	0.467
r_symmetry_vdw_refined	0.295
r_symmetry_vdw_other	0.288
r_xyhbond_nbd_refined	0.219
r_nbd_refined	0.202
r_nbd_other	0.186
r_nbtor_refined	0.173
r_chiral_restr	0.121
r_nbtor_other	0.081
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4444
Nucleic Acid Atoms
Solvent Atoms	479
Heterogen Atoms	42

Software

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