3KHZ

Crystal Structure of R350A mutant of Staphylococcus aureus metallopeptidase (Sapep/DapE) in the apo-form

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	Microbatch method under oil	6.5	293	0.2M Ammonium Sulfate, 0.1M MES, 30.0% PEG Mono-methyl-ether 5000, pH 6.5, Microbatch method under oil, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.64	53.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.75	α = 90
b = 133.52	β = 95.59
c = 67.71	γ = 90

Symmetry
Space Group	P 1 21 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	IMAGE PLATE	MAR scanner 345 mm plate	OSMIC MIRROR	2009-04-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	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	2.5	60.16	100	0.068	0.072	20.9	8.5		39597	2	2	58.5

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	2.5	2.64	100		0.414	0.442	4.9	8.4	5730

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	2.5	49.02	37576	1984	99.97	0.21077	0.20776	0.2693	RANDOM	49.954

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]
-0.4		-1.75	-2.31		2.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.307
r_dihedral_angle_4_deg	22.597
r_dihedral_angle_3_deg	18.953
r_dihedral_angle_1_deg	6.386
r_scangle_it	2.619
r_scbond_it	1.627
r_angle_refined_deg	1.35
r_mcangle_it	1.111
r_mcbond_it	0.588
r_chiral_restr	0.097

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.307
r_dihedral_angle_4_deg	22.597
r_dihedral_angle_3_deg	18.953
r_dihedral_angle_1_deg	6.386
r_scangle_it	2.619
r_scbond_it	1.627
r_angle_refined_deg	1.35
r_mcangle_it	1.111
r_mcbond_it	0.588
r_chiral_restr	0.097
r_bond_refined_d	0.011
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6767
Nucleic Acid Atoms
Solvent Atoms	113
Heterogen Atoms

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.