8RTZ | pdb_00008rtz

The structure of E. coli penicillin binding protein 3 (PBP3) in complex with a bicyclic peptide inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6I1I	Piperacillin was removed

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	277	0.1M Tris pH 9.0 and 20% (w/v) PEG 6K supplemented with an additive, 30% (w/v) dextran sulphate sodium salt, Mr 5K

Crystal Properties
Matthews coefficient	Solvent content
2.11	42.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.89	α = 90
b = 152.181	β = 90
c = 43.675	γ = 90

Symmetry
Space Group	C 2 2 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 PILATUS 2M		2020-04-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.000	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.52	45.04	99.6	1	23.8	12.2		50525

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.52	1.55	93		0.749		7.1

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.52	45.04	50510	2525	99.58	0.184	0.1819	0.19	0.2157	0.23	24.42

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]
3.04			-1.971		-1.069

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.319
r_dihedral_angle_other_3_deg	17.939
r_dihedral_angle_4_deg	14.285
r_dihedral_angle_3_deg	13.146
r_dihedral_angle_1_deg	6.815
r_lrange_it	6.377
r_lrange_other	6.376
r_scangle_it	4.376
r_scangle_other	4.375
r_mcangle_it	3.241
r_mcangle_other	3.241
r_scbond_it	2.848
r_scbond_other	2.847
r_mcbond_it	2.174
r_mcbond_other	2.169
r_angle_refined_deg	1.738
r_angle_other_deg	1.438
r_symmetry_nbd_refined	0.348
r_nbd_other	0.262
r_nbd_refined	0.228
r_xyhbond_nbd_refined	0.188
r_symmetry_nbd_other	0.187
r_nbtor_refined	0.17
r_symmetry_xyhbond_nbd_refined	0.164
r_chiral_restr	0.09
r_symmetry_nbtor_other	0.084
r_symmetry_xyhbond_nbd_other	0.075
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2525
Nucleic Acid Atoms
Solvent Atoms	263
Heterogen Atoms	18

Software

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