3QFH | pdb_00003qfh

2.05 Angstrom Resolution Crystal Structure of Epidermin Leader Peptide Processing Serine Protease (EpiP) from Staphylococcus aureus.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1THM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	295	Protein: 7mg/mL, ?M Sodium cloride, Tris-HCl (pH 8.3), Screen: GCSG+ (H9), 0.2M Lithium sulfate, 0.1M Bis-Tris pH 5.5, 25% (w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.505	α = 89.98
b = 94.696	β = 90.37
c = 122.999	γ = 116.79

Symmetry
Space Group	P 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	MARMOSAIC 225 mm CCD	Beryllium lenses	2010-11-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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	2.05	30	97.9	0.047	15	2	219399	219399		-3	30.9

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)
	2.05	2.09	97		0.354	2.1	2	10837

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	1THM	2.05	29.69	200752	200752	10599	97.82	0.1718	0.1718	0.1695	0.18	0.21596	0.23	RANDOM	38.607

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]
-1.78	-2.15	-0.19	1.41	0.13	-1.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.189
r_dihedral_angle_4_deg	10.99
r_dihedral_angle_3_deg	10.394
r_scangle_it	4.668
r_dihedral_angle_1_deg	3.107
r_scbond_it	2.976
r_mcangle_it	1.797
r_angle_refined_deg	1.353
r_mcbond_it	1.018
r_angle_other_deg	0.834

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.189
r_dihedral_angle_4_deg	10.99
r_dihedral_angle_3_deg	10.394
r_scangle_it	4.668
r_dihedral_angle_1_deg	3.107
r_scbond_it	2.976
r_mcangle_it	1.797
r_angle_refined_deg	1.353
r_mcbond_it	1.018
r_angle_other_deg	0.834
r_mcbond_other	0.297
r_chiral_restr	0.085
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	26598
Nucleic Acid Atoms
Solvent Atoms	1511
Heterogen Atoms	221

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	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.