3BF0

Crystal structure of Escherichia coli Signal peptide peptidase (SppA), Native crystals

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	PEG3350, pH 7.5, vapor diffusion, hanging drop, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.76	55.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.171	α = 90
b = 153.485	β = 104.25
c = 100.659	γ = 90

Symmetry
Space Group	P 1 21 1

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	mirrors		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4A	0.97925	NSLS	X4A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.5	50	96.2	0.122	0.122	16	7.2	86579	86579

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.5	2.6	80.8		0.324	0.32	3.2	6	7232

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	MOLECULAR REPLACEMENT	THROUGHOUT	2.55	50	86551	4338	96.16	0.217	0.214	0.252	RANDOM	28.947

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]
2.3		1.8	-1.84		0.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.861
r_dihedral_angle_3_deg	19.427
r_dihedral_angle_4_deg	17.424
r_dihedral_angle_1_deg	7.726
r_scangle_it	3.586
r_scbond_it	2.196
r_angle_refined_deg	1.765
r_mcangle_it	1.474
r_mcbond_it	0.877
r_nbtor_refined	0.314

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.861
r_dihedral_angle_3_deg	19.427
r_dihedral_angle_4_deg	17.424
r_dihedral_angle_1_deg	7.726
r_scangle_it	3.586
r_scbond_it	2.196
r_angle_refined_deg	1.765
r_mcangle_it	1.474
r_mcbond_it	0.877
r_nbtor_refined	0.314
r_nbd_refined	0.232
r_xyhbond_nbd_refined	0.156
r_symmetry_vdw_refined	0.152
r_chiral_restr	0.122
r_symmetry_hbond_refined	0.094
r_bond_refined_d	0.016
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14377
Nucleic Acid Atoms
Solvent Atoms	488
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.