1OBZ | pdb_00001obz

Crystal structure of the complex of the PDZ tandem of syntenin with an interleukin 5 receptor alpha peptide.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1N99	PDB ENTRY 1N99

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6		SITTING DROP WITH 0.2 M SODIUM ACETATE, PH 4.6 28% PEG4000, 0.2 M AMMONIUM ACETATE

Crystal Properties
Matthews coefficient	Solvent content
2.2	43.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.485	α = 90
b = 48.172	β = 120.24
c = 74.996	γ = 90

Symmetry
Space Group	C 1 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		2002-01-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X9B		NSLS	X9B

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	1.7	50	95.7	0.044	25.4	3.4		112090

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	1.7	1.76	72.4		0.287	3.13

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-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 1N99	1.7	64.55	32205	1048	95.8	0.148	0.16	0.213	0.22	RANDOM	12.64

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]
		-0.01	0.02		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.059
r_scangle_it	4.302
r_scbond_it	2.72
r_mcangle_it	1.932
r_angle_refined_deg	1.507
r_mcbond_it	1.153
r_angle_other_deg	0.807
r_symmetry_vdw_other	0.308
r_nbd_other	0.254
r_nbd_refined	0.226
r_xyhbond_nbd_refined	0.203
r_symmetry_hbond_refined	0.17
r_symmetry_vdw_refined	0.151
r_chiral_restr	0.089
r_nbtor_other	0.082
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_gen_planes_other	0.003
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2522
Nucleic Acid Atoms
Solvent Atoms	658
Heterogen Atoms	16

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing