6TII

Crystal structure of penicillin-binding protein 2 from Yersinia pestis

X-RAY DIFFRACTION

---

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	1 uL of 1 mg/ml YpPBP2 (in 20 mM Tris-HCl pH 7.5, 150 mM NaCl, 2 mM mecillinam) and 2 uL reservoir solution (containing 0.1 M HEPES-NaOH pH 7.5, 0.5 M K+/Na+ tartrate and 10 mM NaBr)

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.661	α = 113.467
b = 84.773	β = 94.972
c = 88.359	γ = 103.725

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 PILATUS 6M		2018-06-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.976	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.2	79.36	90.2	0.133	0.163	0.095	0.781	6.7	5.5		56420

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	2.2	2.26	87.8		0.827	0.756	0.632	0.703	1.9

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	2.26	50.005	52196	2616	90.395	0.194	0.1914	0.2525	50.592

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]
-2.724	-4.025	-3.875	0.136	1.946	2.622

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.256
r_dihedral_angle_4_deg	20.905
r_dihedral_angle_3_deg	17.271
r_dihedral_angle_1_deg	11.411
r_lrange_it	9.728
r_lrange_other	9.714
r_scangle_it	7.002
r_scangle_other	7.002
r_mcangle_it	6.389
r_mcangle_other	6.389
r_scbond_it	4.558
r_scbond_other	4.557
r_mcbond_it	4.272
r_mcbond_other	4.267
r_angle_refined_deg	1.554
r_angle_other_deg	1.222
r_symmetry_xyhbond_nbd_refined	0.296
r_nbd_other	0.248
r_nbd_refined	0.192
r_symmetry_nbd_refined	0.192
r_symmetry_nbd_other	0.184
r_xyhbond_nbd_refined	0.177
r_nbtor_refined	0.163
r_symmetry_xyhbond_nbd_other	0.117
r_ncsr_local_group_1	0.101
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.067
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8420
Nucleic Acid Atoms
Solvent Atoms	305
Heterogen Atoms	2

Software

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