7ZUI

PENICILLIN-BINDING PROTEIN 1B (PBP-1B) in complex with lactone 5Az - 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
3.3	62.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.025	α = 90
b = 149.061	β = 90
c = 99.226	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	1.568	48.02	99.3	0.067	0.997	10.62	4.7		98508			34.821

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	1.568	1.66	99.4		1.221	0.447	1.09	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	1.57	48.013	98507	2458	99.343	0.155	0.1538	0.1814	41.839

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]
0.293			0.091		-0.384

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.69
r_dihedral_angle_4_deg	13.004
r_dihedral_angle_3_deg	12.022
r_lrange_it	7.954
r_lrange_other	7.801
r_dihedral_angle_1_deg	7.105
r_scangle_it	5.846
r_scangle_other	5.845
r_scbond_it	4.087
r_scbond_other	4.086
r_mcangle_it	2.628
r_mcangle_other	2.628
r_mcbond_it	2.126
r_mcbond_other	2.126
r_angle_other_deg	1.419
r_angle_refined_deg	1.245
r_symmetry_xyhbond_nbd_refined	0.288
r_nbd_refined	0.209
r_nbd_other	0.2
r_symmetry_nbd_other	0.192
r_symmetry_nbd_refined	0.19
r_nbtor_refined	0.172
r_xyhbond_nbd_refined	0.154
r_symmetry_nbtor_other	0.088
r_chiral_restr	0.073
r_xyhbond_nbd_other	0.033
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_chiral_restr_other
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3506
Nucleic Acid Atoms
Solvent Atoms	589
Heterogen Atoms	51

Software

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