5DVY

2.95 Angstrom Crystal Structure of the Dimeric Form of Penicillin Binding Protein 2 Prime from Enterococcus faecium

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	295	Protein: 12.4 mg/ml, 0.01M Tris-HCL (pH 8.3), Screen: Classics II (A3), 0.1M Bis-Tris (pH 5.5), 2M Ammonium sulfate, Cryo: 25% Sucrose, 2M Ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
5.82	78.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 193.162	α = 90
b = 193.162	β = 90
c = 156.478	γ = 120

Symmetry
Space Group	P 63 2 2

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		2015-03-09	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	2.95	30	99.8	0.13	0.13	23.7	13.2		36548		-3	68.2

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	2.95	3	100		0.69	4	13.5

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	2.95	29.91	34772	1762	99.45	0.15437	0.1527	0.18678	RANDOM	62.27

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]
-0.11	-0.06		-0.11		0.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.647
r_dihedral_angle_4_deg	10.942
r_dihedral_angle_3_deg	9.395
r_long_range_B_refined	7.915
r_long_range_B_other	7.915
r_scangle_other	5.952
r_scbond_it	4.215
r_scbond_other	4.194
r_mcangle_it	3.758
r_mcangle_other	3.757
r_mcbond_it	2.327
r_mcbond_other	2.326
r_dihedral_angle_1_deg	2.052
r_angle_refined_deg	1.515
r_angle_other_deg	0.746
r_chiral_restr	0.088
r_gen_planes_refined	0.022
r_gen_planes_other	0.019
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	4898
Nucleic Acid Atoms
Solvent Atoms	243
Heterogen Atoms	78

Software

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