3BEZ

Crystal structure of Escherichia coli Signal peptide peptidase (SppA), SeMet 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
2.68	54.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.022	α = 90
b = 153.04	β = 104.17
c = 100.214	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	2.76	46.9	97.8	0.178	0.178	15.6	7.4		69169

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)
1	2.76	2.9	78		0.45	0.33	3.3	6.1	5523

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	2.76	46.63	69168	3502	100	0.203	0.2	0.259	RANDOM	25.373

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]
1.98		2.51	-1.84		1.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.429
r_dihedral_angle_3_deg	20.497
r_dihedral_angle_4_deg	18.842
r_dihedral_angle_1_deg	10.396
r_scangle_it	3.619
r_scbond_it	2.238
r_angle_refined_deg	1.892
r_mcangle_it	1.361
r_mcbond_it	0.868
r_nbtor_refined	0.324

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.429
r_dihedral_angle_3_deg	20.497
r_dihedral_angle_4_deg	18.842
r_dihedral_angle_1_deg	10.396
r_scangle_it	3.619
r_scbond_it	2.238
r_angle_refined_deg	1.892
r_mcangle_it	1.361
r_mcbond_it	0.868
r_nbtor_refined	0.324
r_nbd_refined	0.252
r_symmetry_vdw_refined	0.189
r_xyhbond_nbd_refined	0.169
r_symmetry_hbond_refined	0.155
r_chiral_restr	0.129
r_bond_refined_d	0.017
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14362
Nucleic Acid Atoms
Solvent Atoms	627
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SHELXD	phasing

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.