7O4B

Crystal structure of Penicillin-Binding Protein 1 (PBP1) from Staphylococcus aureus in complex with penicillin G

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5TRO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291.15	sodium citrate

Crystal Properties
Matthews coefficient	Solvent content
3.61	65.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 180.649	α = 90
b = 180.649	β = 90
c = 223.466	γ = 120

Symmetry
Space Group	P 64 2 2

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 PILATUS3 6M		2020-07-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.97918	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	2.593	47.513	96.3	0.147	0.03	22.1	24.7		45182

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.593	2.846			2.163	0.42

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	5TRO	2.593	47.505	45181	2318	67.427	0.207	0.2048	0.2415	63.226

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]
-0.084	-0.042		-0.084		0.273

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.978
r_dihedral_angle_3_deg	20.416
r_dihedral_angle_4_deg	19.05
r_lrange_other	11.96
r_lrange_it	11.957
r_scangle_it	9.043
r_scangle_other	9.019
r_mcangle_it	8.623
r_mcangle_other	8.623
r_dihedral_angle_1_deg	7.014
r_scbond_it	5.866
r_scbond_other	5.825
r_mcbond_it	5.673
r_mcbond_other	5.664
r_angle_refined_deg	1.566
r_angle_other_deg	1.208
r_symmetry_xyhbond_nbd_refined	0.427
r_nbd_other	0.215
r_nbd_refined	0.207
r_symmetry_nbd_other	0.191
r_symmetry_nbd_refined	0.182
r_nbtor_refined	0.169
r_xyhbond_nbd_refined	0.155
r_chiral_restr_other	0.142
r_ncsr_local_group_1	0.114
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.065
r_symmetry_xyhbond_nbd_other	0.023
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7755
Nucleic Acid Atoms
Solvent Atoms	39
Heterogen Atoms	94

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
STARANISO	data scaling
MOLREP	phasing