5TRO

1.8 Angstrom Resolution Crystal Structure of Dimerization and Transpeptidase domains (residues 39-608) of Penicillin-Binding Protein 1 from Staphylococcus aureus.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.3	295	Protein: 10.8 mg/ml, 0.5M Sodium chloride, 0.01M Tris HCl (pH 8.3), Screen: JCSG+ (A5), 0.2M Magnesium formate, 20% (w/v) PEG 3350.

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 178.843	α = 90
b = 72.202	β = 103.18
c = 86.362	γ = 90

Symmetry
Space Group	C 1 2 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 300 mm CCD	C(111)	2016-10-20	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)	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	1.8	30	99.7	0.088	0.088	26.8	5.4		98204		-3	30.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.83	99.3		0.749	0.793	2.3	4.9

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	SAD	THROUGHOUT	1.8	29.59	93238	4950	99.22	0.18088	0.17935	0.20946	RANDOM	43.7

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]
0.34		-1.07	-1.38		1.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.828
r_dihedral_angle_4_deg	10.696
r_dihedral_angle_3_deg	10.411
r_long_range_B_refined	5.186
r_long_range_B_other	5.028
r_dihedral_angle_1_deg	3.139
r_scangle_other	1.941
r_mcangle_it	1.739
r_mcangle_other	1.739
r_angle_refined_deg	1.365
r_scbond_it	1.183
r_scbond_other	1.183
r_mcbond_it	1.066
r_mcbond_other	1.065
r_angle_other_deg	0.819
r_chiral_restr	0.085
r_gen_planes_refined	0.021
r_gen_planes_other	0.017
r_bond_refined_d	0.009
r_bond_other_d	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7959
Nucleic Acid Atoms
Solvent Atoms	615
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing