7ZG8

Crystal structure of A. baumannii penicillin-binding protein 2

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, SITTING DROP	4.2	291	0.1M Na2HPO4 adjusted to pH 4.2 with citric acid, 16% (v/v) ethanol, and 5% (w/v) PEG 1000

Crystal Properties
Matthews coefficient	Solvent content
2.87	57.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.249	α = 90
b = 151.03	β = 90
c = 177.369	γ = 90

Symmetry
Space Group	I 2 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	PIXEL	DECTRIS PILATUS3 6M		2018-07-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97625	Diamond	I03

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	2.65	44.34	98.7	0.203	0.213	0.065	0.994	9	9.7		46823

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	2.65	2.74	99.4		1.108	1.167	0.36	0.754	2	9.7

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	2.65	44.334	46819	2395	98.388	0.213	0.211	0.2523	61.653

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]
9			-2.868		-6.132

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.157
r_dihedral_angle_3_deg	17.275
r_dihedral_angle_4_deg	14.104
r_lrange_other	9.799
r_lrange_it	9.798
r_mcangle_it	7.272
r_mcangle_other	7.272
r_dihedral_angle_1_deg	7.052
r_scangle_it	6.681
r_scangle_other	6.68
r_mcbond_it	4.552
r_mcbond_other	4.552
r_scbond_it	4.042
r_scbond_other	4.041
r_angle_refined_deg	1.525
r_angle_other_deg	1.195
r_symmetry_nbd_refined	0.277
r_nbd_refined	0.171
r_nbtor_refined	0.156
r_xyhbond_nbd_refined	0.152
r_symmetry_nbd_other	0.148
r_nbd_other	0.124
r_ncsr_local_group_1	0.09
r_symmetry_nbtor_other	0.075
r_symmetry_xyhbond_nbd_refined	0.074
r_chiral_restr	0.062
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8071
Nucleic Acid Atoms
Solvent Atoms	113
Heterogen Atoms	2

Software

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