1ZB5 | pdb_00001zb5

Recognition of peptide ligands by signalling protein from porcine mammary gland (SPP-40): Crystal structure of the complex of SPP-40 with a peptide Trp-Pro-Trp at 2.45A resolution

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.8	298	25mM tris-HCl, 11% ethanol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.38	α = 90
b = 66.79	β = 90
c = 107.66	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	IMAGE PLATE	MARRESEARCH	MIRROR	2004-10-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.45	20	95.2	0.077	9.7		17202	16643			26.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.45	2.49	96.1		0.412	2.2

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 (All)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1xrv	2.45	20	17202	16304	339	95.2	0.194	0.193	0.192	0.226	RANDOM	33.8

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]
-2.58			-2.44		5.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	24.6
x_scangle_it	4.711
x_mcangle_it	3.298
x_scbond_it	3.187
x_mcbond_it	1.998
r_angle_refined_deg	1.6
x_dihedral_angle_d	1.11
r_bond_refined_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2947
Nucleic Acid Atoms
Solvent Atoms	138
Heterogen Atoms	28

Software

Software
Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.