8VEP

Crystal structure of transpeptidase domain of PBP2 from Neisseria gonorrhoeae cephalosporin-resistant strain H041 acylated by piperacillin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6VBC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9.8	291	32-40% PEG 600, 0.1 M CHES

Crystal Properties
Matthews coefficient	Solvent content
2.3	45.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.621	α = 90
b = 61.621	β = 90
c = 110.534	γ = 90

Symmetry
Space Group	P 21 21 21

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 EIGER X 16M		2022-06-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1	APS	22-ID

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	46.07	99.3	0.177	0.074	0.99	9.9	6.6		23839			16.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.07	98.5		0.552	0.246	0.829	2.3	5.8

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 (All)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	2.002	46.07	23837	1158	99.3	0.172	0.17	0.206	RANDOM	17.513

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]
0.73			-0.992		0.262

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.379
r_dihedral_angle_3_deg	13.271
r_dihedral_angle_2_deg	9.466
r_dihedral_angle_1_deg	6.651
r_lrange_it	4.968
r_lrange_other	4.935
r_scangle_it	3.65
r_scangle_other	3.649
r_mcangle_it	2.442
r_mcangle_other	2.441
r_scbond_it	2.267
r_scbond_other	2.266
r_angle_refined_deg	1.613
r_mcbond_it	1.581
r_mcbond_other	1.581
r_angle_other_deg	0.5
r_nbd_refined	0.209
r_symmetry_nbd_other	0.18
r_nbtor_refined	0.176
r_symmetry_xyhbond_nbd_refined	0.176
r_xyhbond_nbd_refined	0.157
r_nbd_other	0.096
r_symmetry_nbtor_other	0.088
r_chiral_restr	0.073
r_symmetry_nbd_refined	0.055
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	2453
Nucleic Acid Atoms
Solvent Atoms	185
Heterogen Atoms	43

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
HKL-2000	data reduction
REFMAC	phasing