3IL0

The crystal structure of the aminopeptidase P,XAA-pro aminopeptidase from Streptococcus thermophilus

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1			289	0.2M Calcium acetate hydrate, 20% w/v PEG 3350, 25% glycerol, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.89	57.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.303	α = 90
b = 80.396	β = 90
c = 100.858	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	100	CCD	ADSC QUANTUM 315r	mirrors	2009-06-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9794	APS	19-ID

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	2.2	62.87	99.58	0.133	24.1	8.9	17595	17521	2	2

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	2.257	99.63		0.64	1.89	7.3	1345

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	2.2	62.87	17521	947	99.58	0.20314	0.20132	0.23688	RANDOM	26.023

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]
0.14			1.4		-1.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.471
r_dihedral_angle_4_deg	19.392
r_dihedral_angle_3_deg	17.538
r_dihedral_angle_1_deg	6.526
r_scangle_it	5.322
r_scbond_it	3.284
r_mcangle_it	2.305
r_angle_refined_deg	1.929
r_mcbond_it	1.228
r_angle_other_deg	1.041

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.471
r_dihedral_angle_4_deg	19.392
r_dihedral_angle_3_deg	17.538
r_dihedral_angle_1_deg	6.526
r_scangle_it	5.322
r_scbond_it	3.284
r_mcangle_it	2.305
r_angle_refined_deg	1.929
r_mcbond_it	1.228
r_angle_other_deg	1.041
r_mcbond_other	0.279
r_chiral_restr	0.121
r_bond_refined_d	0.024
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2096
Nucleic Acid Atoms
Solvent Atoms	64
Heterogen Atoms	12

Software

Software
Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

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 R01GM133198.