3KI9

Crystal structure of Staphylococcus aureus metallopeptidase (Sapep/DapE) in the Mn2+ bound form

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3KHX	PDB ENTRY 3KHX, independent domains

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	Microbatch method under oil	6.8	293	0.2M Megnesium Acetate tetrahydrate, 0.1M Sodium Cacodylate pH 6.8, 22.0% Polyethylene glycol 8000, Microbatch method under oil, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.98	58.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 158.15	α = 90
b = 158.15	β = 90
c = 158.15	γ = 90

Symmetry
Space Group	I 2 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU		2009-07-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	OTHER	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.9	50	100	0.108	0.115	14.2	7.9		14758	2	2	69.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.9	3.06	100		0.563	0.604	3.6	7.8	2141

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3KHX, independent domains	2.9	28.88	13998	745	99.99	0.20492	0.20212	0.2626	RANDOM	42.555

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.888
r_dihedral_angle_4_deg	20.69
r_dihedral_angle_3_deg	15.345
r_dihedral_angle_1_deg	4.845
r_scangle_it	1.232
r_angle_refined_deg	0.937
r_scbond_it	0.695
r_mcangle_it	0.577
r_mcbond_it	0.304
r_chiral_restr	0.065

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.888
r_dihedral_angle_4_deg	20.69
r_dihedral_angle_3_deg	15.345
r_dihedral_angle_1_deg	4.845
r_scangle_it	1.232
r_angle_refined_deg	0.937
r_scbond_it	0.695
r_mcangle_it	0.577
r_mcbond_it	0.304
r_chiral_restr	0.065
r_bond_refined_d	0.005
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3662
Nucleic Acid Atoms
Solvent Atoms	26
Heterogen Atoms	7

Software

Software
Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	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 R01GM133198.