1W9E

Crystal structure of the PDZ tandem of human syntenin in complex with TNEFYF peptide

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5		20% PEG3350, 0.2M NH4CL, VAPOR DIFFUSION, SITTING DROP, pH 7.50

Crystal Properties
Matthews coefficient	Solvent content
2.3	49.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.207	α = 90
b = 72.207	β = 90
c = 126.046	γ = 90

Symmetry
Space Group	P 41 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	CCD	ADSC CCD		2003-09-10	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	1.56	30	100	0.063	39.93	9.9		48061

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	1.56	1.63	99.9		0.525	4.25	9.43

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1N99	1.56	63.25	47197	989	100	0.172	0.171	0.201	RANDOM	19.65

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]
-0.26			-0.26		0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.199
r_scangle_it	5.332
r_scbond_it	3.681
r_mcangle_it	2.541
r_mcbond_it	1.637
r_angle_refined_deg	1.494
r_angle_other_deg	0.842
r_symmetry_vdw_other	0.319
r_symmetry_hbond_refined	0.266
r_nbd_other	0.26
r_symmetry_vdw_refined	0.252
r_nbd_refined	0.228
r_xyhbond_nbd_refined	0.212
r_chiral_restr	0.095
r_nbtor_other	0.083
r_bond_refined_d	0.017
r_gen_planes_other	0.01
r_gen_planes_refined	0.008
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	2652
Nucleic Acid Atoms
Solvent Atoms	376
Heterogen Atoms	9

Software

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