3IFE | pdb_00003ife

1.55 Angstrom Resolution Crystal Structure of Peptidase T (pepT-1) from Bacillus anthracis str. 'Ames Ancestor'.

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	295	Protein solution: 7.5mg/mL, 0.25M NaCl, Tris-HCl pH(8.3); Screen solution: JCSG+, E2, 0.2M NaCl, 2M Ammonium sulfate, 0.1M Na-Cacodilate pH(6.5) VAPOR DIFFUSION, SITTING DROP, temperature 295K; Cryo: 25% Sucrose, 1.8M Ammonium sulfate.

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.216	α = 90
b = 142.739	β = 90
c = 40.993	γ = 90

Symmetry
Space Group	P 21 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	MARMOSAIC 300 mm CCD	Beryllium lenses	2009-07-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

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	1.55	30	99.9	0.068	25.8	7.3	77209	77209		-3	21

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	1.55	1.58	99.3		0.554	3.3	6.5	3814

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1fno	1.55	29.11	73110	73110	3863	99.94	0.14954	0.14954	0.14836	0.17	0.17173	0.2	RANDOM	12.404

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]
-1.09			-0.36		1.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.925
r_dihedral_angle_4_deg	13.661
r_dihedral_angle_3_deg	9.079
r_scangle_it	4.329
r_dihedral_angle_1_deg	3.19
r_scbond_it	2.664
r_angle_refined_deg	1.493
r_mcangle_it	1.481
r_angle_other_deg	0.879
r_mcbond_it	0.854

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.925
r_dihedral_angle_4_deg	13.661
r_dihedral_angle_3_deg	9.079
r_scangle_it	4.329
r_dihedral_angle_1_deg	3.19
r_scbond_it	2.664
r_angle_refined_deg	1.493
r_mcangle_it	1.481
r_angle_other_deg	0.879
r_mcbond_it	0.854
r_mcbond_other	0.288
r_chiral_restr	0.098
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3282
Nucleic Acid Atoms
Solvent Atoms	586
Heterogen Atoms	59

Software

Software
Software Name	Purpose
Blu-Ice	data collection
CRANK	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	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 R01GM157729.