9MD0 | pdb_00009md0

Crystal structure of the transpeptidase domain of PBP2 from the Neisseria gonorrhoeae cephalosporin decreased susceptibility strain 35/02 in complex with boronate inhibitor VNRX-6752

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9.3	291	40% PEG 600, 0.1 M CHES, PH 9.3

Crystal Properties
Matthews coefficient	Solvent content
2.4	49.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.464	α = 90
b = 60.224	β = 90
c = 110.34	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		2020-10-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.00	APS	22-ID

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	2.6	38.7	98.9	0.199	0.215	0.08	0.988	14.1	7.2		10571			29.1

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	2.6	2.7	94.3		0.713	0.769	0.283	0.831	4.2	7.4

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	2.613	38.68	10570	514	98.85	0.178	0.1749	0.1809	0.2319	0.2307	RANDOM	28.8

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]
0.113			-0.149		0.037

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.555
r_dihedral_angle_3_deg	14.713
r_dihedral_angle_2_deg	7.623
r_dihedral_angle_1_deg	7.545
r_lrange_it	6.334
r_lrange_other	6.333
r_scangle_it	4.874
r_scangle_other	4.872
r_mcangle_it	3.916
r_mcangle_other	3.914
r_scbond_it	3.155
r_scbond_other	3.155
r_mcbond_other	2.504
r_mcbond_it	2.503
r_angle_refined_deg	1.57
r_angle_other_deg	0.518
r_nbd_other	0.218
r_nbd_refined	0.217
r_symmetry_xyhbond_nbd_refined	0.208
r_symmetry_nbd_other	0.193
r_nbtor_refined	0.18
r_symmetry_nbd_refined	0.149
r_xyhbond_nbd_refined	0.102
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.068
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2450
Nucleic Acid Atoms
Solvent Atoms	19
Heterogen Atoms	40

Software

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