8CF3 | pdb_00008cf3

Crystal structure of S. aureus BlaR1 sensor domain in complex with cefepime

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1XA7	BlaR1 sensor domain apo structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.25	291	Soidum Cacodylate 0.085M pH 5.5 + PEG 8K 27% + Glycerol 15%

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.819	α = 90
b = 109.47	β = 103.657
c = 50.297	γ = 90

Symmetry
Space Group	P 1 21 1

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 6M		2021-12-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	1.0064	ALBA	XALOC

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	2.153	45.537	82.55	0.13	0.142	0.057	0.9969	9.186	6.05		17584

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.153	2.345			1.772	0.865	0.3028

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	FREE R-VALUE	2.52	45.537	15112	778	90.605	0.219	0.2165	0.2143	0.27	0.2636	54.16

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]
-0.294		3.124	3.39		-4.127

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.567
r_dihedral_angle_6_deg	13.85
r_dihedral_angle_1_deg	6.113
r_lrange_it	3.507
r_lrange_other	3.483
r_dihedral_angle_2_deg	3.438
r_mcangle_it	2.012
r_mcangle_other	2.012
r_scangle_it	1.679
r_scangle_other	1.679
r_mcbond_it	1.113
r_mcbond_other	1.113
r_angle_refined_deg	0.917
r_scbond_it	0.91
r_scbond_other	0.91
r_angle_other_deg	0.338
r_nbd_other	0.237
r_symmetry_xyhbond_nbd_refined	0.202
r_nbd_refined	0.192
r_symmetry_nbd_other	0.187
r_nbtor_refined	0.186
r_xyhbond_nbd_refined	0.165
r_symmetry_nbd_refined	0.129
r_ncsr_local_group_1	0.08
r_chiral_restr	0.079
r_symmetry_nbtor_other	0.076
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4140
Nucleic Acid Atoms
Solvent Atoms	59
Heterogen Atoms	76

Software

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