1YBO

Crystal structure of the PDZ tandem of human syntenin with syndecan peptide

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP			20% PEG 3350, 0.2M NH4Cl, VAPOR DIFFUSION, SITTING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.3	49.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.322	α = 90
b = 72.322	β = 90
c = 125.921	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 QUANTUM 4		2003-04-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X8C	0.97960	NSLS	X8C

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	2	40	99	0.07	30.3	8.3		23083			25.7

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	2	2.07	100		0.283	8.31	7.9	2282

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 (All)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1N99	2.3	40	15391	800	99.28	0.197	0.193	0.273	RANDOM	25.247

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]
-0.53			-0.53		1.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.271
r_dihedral_angle_4_deg	22.434
r_dihedral_angle_3_deg	14.39
r_dihedral_angle_1_deg	5.735
r_angle_refined_deg	2.613
r_scangle_it	2.246
r_angle_other_deg	1.484
r_scbond_it	1.477
r_mcbond_it	1.022
r_mcangle_it	0.928
r_symmetry_hbond_refined	0.274
r_symmetry_vdw_other	0.211
r_nbd_refined	0.194
r_xyhbond_nbd_refined	0.175
r_nbd_other	0.174
r_nbtor_refined	0.159
r_symmetry_vdw_refined	0.118
r_chiral_restr	0.096
r_mcbond_other	0.093
r_nbtor_other	0.085
r_xyhbond_nbd_other	0.015
r_bond_refined_d	0.011
r_bond_other_d	0.006
r_gen_planes_refined	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2580
Nucleic Acid Atoms
Solvent Atoms	190
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
AMoRE	phasing