3RZA

Crystal structure of a tripeptidase (SAV1512) from staphylococcus aureus subsp. aureus mu50 at 2.10 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.43	293	20.0% 2-propanol, 20.0% polyethylene glycol 4000, 0.1M sodium citrate - citric acid pH 5.43, Additive: 0.006 M zinc chloride, 0.006 M calcium chloride, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.996	α = 89.67
b = 57.805	β = 73.38
c = 79.857	γ = 72.36

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 325 mm CCD	double crystal monochromator	2010-03-12	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91162,0.97936,0.97911	SSRL	BL9-2

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	2.1	29.517	88.6	0.139	4.89	1.99		43307		-3	24.476

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	2.09	2.16	73.4		0.657	1.4

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	MAD	THROUGHOUT	2.1	29.517	43307	2176	96.42	0.169	0.1668	0.2123	RANDOM	25.5159

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]
-0.18	-0.1	0.14	0.12	-0.29	0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.985
r_dihedral_angle_4_deg	18.777
r_dihedral_angle_3_deg	13.291
r_dihedral_angle_1_deg	6.876
r_scangle_it	5.322
r_scbond_it	3.508
r_mcangle_it	2.315
r_mcbond_it	1.427
r_angle_refined_deg	1.398
r_angle_other_deg	1.242

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.985
r_dihedral_angle_4_deg	18.777
r_dihedral_angle_3_deg	13.291
r_dihedral_angle_1_deg	6.876
r_scangle_it	5.322
r_scbond_it	3.508
r_mcangle_it	2.315
r_mcbond_it	1.427
r_angle_refined_deg	1.398
r_angle_other_deg	1.242
r_mcbond_other	0.485
r_chiral_restr	0.081
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.005
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5529
Nucleic Acid Atoms
Solvent Atoms	397
Heterogen Atoms	111

Software

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