4WVH | pdb_00004wvh

Crystal structure of the Type-I signal peptidase from Staphylococcus aureus (SpsB) in complex with a substrate peptide (pep1).

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4WVG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE		296	12 % PEG 8000, 20 % ethylene glycol, 100 mM sodium acetate pH 5.3 - 5.5

Crystal Properties
Matthews coefficient	Solvent content
2.62	53.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.661	α = 90
b = 80.193	β = 90
c = 119.426	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 210r		2014-06-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX1	0.9537	Australian Synchrotron	MX1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	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	2.1	66.58	99.9	0.319	0.086	0.994	10			36431

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.16	100		2.622	0.703	0.589	1.6	14.8	2945

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	4WVG	2.1	66.58	34573	1799	99.81	0.2103	0.2083	0.22	0.2485	0.25	RANDOM	29.051

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]
0.29			-0.88		0.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.396
r_dihedral_angle_3_deg	13.308
r_dihedral_angle_4_deg	7.955
r_dihedral_angle_1_deg	5.635
r_mcangle_it	2.028
r_mcbond_it	1.227
r_mcbond_other	1.227
r_angle_refined_deg	1.174
r_angle_other_deg	0.725
r_chiral_restr	0.066

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.396
r_dihedral_angle_3_deg	13.308
r_dihedral_angle_4_deg	7.955
r_dihedral_angle_1_deg	5.635
r_mcangle_it	2.028
r_mcbond_it	1.227
r_mcbond_other	1.227
r_angle_refined_deg	1.174
r_angle_other_deg	0.725
r_chiral_restr	0.066
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4075
Nucleic Acid Atoms
Solvent Atoms	246
Heterogen Atoms	23

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data scaling
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

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.