6TIX

Crystal structure of penicillin-binding protein 2 from Yersinia pestis in complex with mecillinam

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5LP4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		296	Crystals were grown in a condition containing 1 uL of 0.8 mg/mL YpPBP2 (in 20 mM Tris-HCl pH 7.5, 150 mM NaCl, 2 mM mecillinam) and 1 uL of reservoir solution (0.45 M Na+/K+ tartrate, 0.1 M HEPES-NaOH pH 7.5, 7.2% PEG 4000). The size of these crystals was optimised by three rounds of macroseeding into condition containing (0.45 M Na+/K+ tartrate, 0.1 M HEPES-NaOH pH 7.5, 7.2% PEG 4000 and 2 mM mecillinam)

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.172	α = 112.917
b = 84.035	β = 95.306
c = 87.099	γ = 104.566

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	PIXEL	DECTRIS PILATUS3 X 2M		2018-04-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.8731	ESRF	ID23-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	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	2.8	45.693	92.9	0.108	0.097	0.991	4.1	2.1		27215

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.95	96.7		0.452	0.64	0.452	0.677	1.2	2.1

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5LP4	2.8	45.693	27076	1308	92.432	0.231	0.228	0.2902	66.303

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]
-4.63	-8.426	-6.118	1.424	4.642	3.222

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.136
r_dihedral_angle_3_deg	18.661
r_dihedral_angle_4_deg	16.094
r_lrange_it	8.632
r_lrange_other	8.631
r_dihedral_angle_1_deg	6.78
r_mcangle_it	5.33
r_mcangle_other	5.329
r_scangle_it	4.728
r_scangle_other	4.727
r_mcbond_it	3.202
r_mcbond_other	3.202
r_scbond_it	2.711
r_scbond_other	2.711
r_angle_refined_deg	1.299
r_angle_other_deg	1.091
r_symmetry_xyhbond_nbd_refined	0.247
r_nbd_other	0.237
r_symmetry_nbd_refined	0.217
r_nbd_refined	0.195
r_symmetry_nbd_other	0.191
r_xyhbond_nbd_refined	0.18
r_nbtor_refined	0.162
r_symmetry_xyhbond_nbd_other	0.121
r_ncsr_local_group_1	0.095
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.046
r_chiral_restr_other	0.035
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8166
Nucleic Acid Atoms
Solvent Atoms	104
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing