4KWB | pdb_00004kwb

Structure of signal peptide peptidase A with C-termini bound in the active sites: insights into specificity, self-processing and regulation

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3BFO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	298.15	100mM TRIS, 23% TERT-BUTANOL UNDER PARAFFIN OIL, VAPOR DIFFUSION, SITTING DROP, temperature 298.15K, pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.797	α = 90
b = 130.979	β = 90
c = 207.099	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	RAYONIX MX-300	VERTICAL COLLIMATING MIRROR	2011-02-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.97949	CLSI	08ID-1

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	2.39	50	99.2	0.06	50.3	6.8	93912	93168	2	-3	51

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	2.39	2.49	97.5		0.302	6.7	6.3	9085

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	3BFO	2.39	50	93310	88919	4708	98.7	0.285	0.208	0.206	0.2	0.24	0.23	RANDOM	50.9

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]
-0.36			1.59		-1.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.134
r_dihedral_angle_3_deg	15.578
r_dihedral_angle_4_deg	14.969
r_dihedral_angle_1_deg	5.257
r_scangle_it	2.576
r_scbond_it	1.524
r_angle_refined_deg	1.061
r_mcangle_it	0.898
r_mcbond_it	0.451
r_chiral_restr	0.069

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.134
r_dihedral_angle_3_deg	15.578
r_dihedral_angle_4_deg	14.969
r_dihedral_angle_1_deg	5.257
r_scangle_it	2.576
r_scbond_it	1.524
r_angle_refined_deg	1.061
r_mcangle_it	0.898
r_mcbond_it	0.451
r_chiral_restr	0.069
r_bond_refined_d	0.008
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14103
Nucleic Acid Atoms
Solvent Atoms	221
Heterogen Atoms

Software

Software
Software Name	Purpose
MxDC	data collection
PHASER	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.