7QXC | pdb_00007qxc

Recognition of Staphylococcus aureus wall teichoic acid analogue SA533 (compound 1) by Fab4461

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5I1D	separate constant and variable domains of PDB entry 5I1D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9.5	294	10 mM Tris-HCl; 250 mM sodium chloride; 12.9 % w/v polyethylene glycol 20,000; 150 mM CAPSO pH 9.5; 6 % v/v polyethylene glycol 300

Crystal Properties
Matthews coefficient	Solvent content
2.8	56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.191	α = 90
b = 65.448	β = 112.899
c = 74.338	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		2020-12-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.97926	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	1.45	53.51	96.6	0.028	0.039	0.027	0.997	16.4	3.1		87656			21.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.45	1.53	80.6		0.43	0.593	0.406	0.608	1.5	2.5

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	separate constant and variable domains of PDB entry 5I1D	1.452	53.51	87588	4368	96.54	0.176	0.1743	0.17	0.1999	0.2	23.016

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]
-0.415		-0.061	0.101		0.269

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.742
r_dihedral_angle_4_deg	21.132
r_dihedral_angle_3_deg	11.908
r_dihedral_angle_1_deg	7.152
r_lrange_it	6.356
r_lrange_other	6.302
r_scangle_it	4.08
r_scangle_other	4.079
r_mcangle_it	3.201
r_mcangle_other	3.2
r_scbond_it	2.613
r_scbond_other	2.613
r_mcbond_it	1.943
r_mcbond_other	1.94
r_angle_refined_deg	1.498
r_angle_other_deg	1.352
r_symmetry_nbd_refined	0.237
r_symmetry_xyhbond_nbd_refined	0.231
r_xyhbond_nbd_refined	0.221
r_nbd_refined	0.197
r_symmetry_nbd_other	0.178
r_nbtor_refined	0.163
r_nbd_other	0.121
r_xyhbond_nbd_other	0.084
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.069
r_symmetry_xyhbond_nbd_other	0.048
r_chiral_restr_other	0.029
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3317
Nucleic Acid Atoms
Solvent Atoms	424
Heterogen Atoms	88

Software

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