7ZUJ

PENICILLIN-BINDING PROTEIN 1B (PBP-1B) in complex with lactone 6Az - Streptococcus pneumoniae R6

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BG1	2BG1 WITHOUT RESIDUES 654 TO 660

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.2	293	50MM HEPES PH 7.2, 3M NACL, 0.6-0.9M AMMONIUM SULFATE

Crystal Properties
Matthews coefficient	Solvent content
3.29	62.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.306	α = 90
b = 149.053	β = 90
c = 98.835	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		2021-06-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.965459	ESRF	MASSIF-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (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	1.535	44.16	98.4	0.131	0.985	5.93	4.8		105235			35.582

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.535	1.63	93.1		1.663	0.325	0.74	4.6

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	2BG1 WITHOUT RESIDUES 654 TO 660	1.55	44.155	102341	2034	99.432	0.166	0.1654	0.1897	42.832

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]
0.906			-0.331		-0.575

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.412
r_dihedral_angle_4_deg	12.095
r_dihedral_angle_3_deg	11.366
r_lrange_it	8.436
r_lrange_other	8.37
r_dihedral_angle_1_deg	6.42
r_scangle_it	5.187
r_scangle_other	5.186
r_scbond_it	3.499
r_scbond_other	3.498
r_mcangle_it	2.451
r_mcangle_other	2.451
r_mcbond_it	1.911
r_mcbond_other	1.911
r_angle_other_deg	1.402
r_angle_refined_deg	1.223
r_xyhbond_nbd_other	0.49
r_symmetry_xyhbond_nbd_refined	0.39
r_symmetry_nbd_refined	0.326
r_nbd_other	0.221
r_nbd_refined	0.21
r_symmetry_nbd_other	0.193
r_nbtor_refined	0.17
r_xyhbond_nbd_refined	0.146
r_symmetry_nbtor_other	0.089
r_chiral_restr	0.062
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3506
Nucleic Acid Atoms
Solvent Atoms	549
Heterogen Atoms	51

Software

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