3EQV

Crystal structure of penicillin-binding protein 2 from Neisseria gonorrhoeae containing four mutations associated with penicillin resistance

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Wild-type structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	294	2.2 M ammonium sulphate, 100 mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
3.84	67.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.6	α = 90
b = 137.2	β = 90
c = 229.8	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	IMAGE PLATE	MAR scanner 300 mm plate		2006-11-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.97934	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.4	50	98	0.101	29.9	7.1	71399	71399			49.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.49	83.5		0.52	2.7	4.3	5957

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	Wild-type structure	2.4	48.1	71366	71366	3558	97.7	0.219	0.219	0.217	0.253	RANDOM	48.7

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]
0.51			-0.15		-0.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.69
r_dihedral_angle_4_deg	19.83
r_dihedral_angle_3_deg	18.09
r_dihedral_angle_1_deg	6.14
r_scangle_it	2.593
r_scbond_it	1.614
r_angle_refined_deg	1.39
r_mcangle_it	1.038
r_mcbond_it	0.604
r_nbtor_refined	0.296

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.69
r_dihedral_angle_4_deg	19.83
r_dihedral_angle_3_deg	18.09
r_dihedral_angle_1_deg	6.14
r_scangle_it	2.593
r_scbond_it	1.614
r_angle_refined_deg	1.39
r_mcangle_it	1.038
r_mcbond_it	0.604
r_nbtor_refined	0.296
r_nbd_refined	0.2
r_symmetry_vdw_refined	0.193
r_symmetry_hbond_refined	0.17
r_xyhbond_nbd_refined	0.137
r_chiral_restr	0.092
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6633
Nucleic Acid Atoms
Solvent Atoms	79
Heterogen Atoms	87

Software

Software
Software Name	Purpose
MAR345	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.