2YD6 | pdb_00002yd6

Crystal structure of the N-terminal Ig1-2 module of Human Receptor Protein Tyrosine Phosphatase Delta

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2YD4	PDB ENTRY 2YD4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.6		0.085M TRI-SODIUM CITRATE DIHYDRATE, 25% PEG 4000, 15% GLYCEROL, PH 5.6 .

Crystal Properties
Matthews coefficient	Solvent content
2.13	44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.71	α = 90
b = 48.71	β = 90
c = 145.91	γ = 120

Symmetry
Space Group	P 32 2 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	ADSC CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02		Diamond	I02

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.35	49	99.9	0.11	17.4	15		45165		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.35	1.4	98.8		0.82	3.1	10.4

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	PDB ENTRY 2YD4	1.35	48.64	42829	2250	99.9	0.142	0.141	0.15	0.171	0.18	RANDOM	12.34

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		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.625
r_dihedral_angle_4_deg	14.246
r_sphericity_free	12.543
r_dihedral_angle_3_deg	11.884
r_sphericity_bonded	7.977
r_dihedral_angle_1_deg	6.704
r_rigid_bond_restr	4.991
r_angle_refined_deg	1.646
r_angle_other_deg	0.855
r_chiral_restr	0.267
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1507
Nucleic Acid Atoms
Solvent Atoms	254
Heterogen Atoms	14

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
XDS	data reduction
xia2	data scaling
SCALA	data scaling
PHASER	phasing