4ME8 | pdb_00004me8

Crystal structure of a signal peptidase I (EF3073) from Enterococcus faecalis V583 at 2.27 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.2	293	20.00% polyethylene glycol 3350, 0.200M ammonium fluoride, No Buffer pH 6.2, Additive: 0.001 M leupeptin, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.73	28.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.488	α = 90
b = 37.488	β = 90
c = 169.046	γ = 90

Symmetry
Space Group	P 41 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 325 mm CCD	Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing)	2011-01-26	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837,0.97944,0.97894	SSRL	BL11-1

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	2.27	28.174	99.4	0.077	11.93			6200		-3	47.346

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	2.27	2.35	99.1		0.777	1.7

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.27	28.174	6146	486	99.53	0.2162	0.2124	0.22	0.258	0.26	RANDOM	61.7506

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]
1.91			1.91		-3.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.677
r_dihedral_angle_3_deg	15.055
r_dihedral_angle_4_deg	11.706
r_dihedral_angle_1_deg	6.606
r_mcangle_it	1.935
r_angle_refined_deg	1.229
r_mcbond_other	1.173
r_mcbond_it	1.172
r_angle_other_deg	0.786
r_chiral_restr	0.076

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.677
r_dihedral_angle_3_deg	15.055
r_dihedral_angle_4_deg	11.706
r_dihedral_angle_1_deg	6.606
r_mcangle_it	1.935
r_angle_refined_deg	1.229
r_mcbond_other	1.173
r_mcbond_it	1.172
r_angle_other_deg	0.786
r_chiral_restr	0.076
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	904
Nucleic Acid Atoms
Solvent Atoms	39
Heterogen Atoms	8

Software

Software
Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
SHELXD	phasing

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.