7QXE | pdb_00007qxe

Recognition of Staphylococcus aureus wall teichoic acid analogue TB87 (compound 3) by Fab4497

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5D6C	PDB entry 5D6C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	294	10 mM MES-NaOH pH 6.2; 0.25 M sodium chloride; 20% (w/v) PEG 4000; 0.1 M Tris-HCl pH 8.5; 0.2 M lithium sulfate

Crystal Properties
Matthews coefficient	Solvent content
3	58.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.033	α = 90
b = 112.915	β = 90
c = 154.993	γ = 90

Symmetry
Space Group	P 21 21 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 6M		2019-12-18	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	1.84	46.98	100	0.085	0.1	0.054	0.999	11.6	6.6		98208			34.1

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	1.84	1.9	100		1.787	2.124	1.135	0.601	0.9	6.5

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	FOURIER SYNTHESIS	FREE R-VALUE	PDB entry 5D6C	1.84	46.004	97934	4988	99.76	0.19	0.1884	0.2	0.2179	0.22	37.866

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]
0.747			1.315		-2.063

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.571
r_dihedral_angle_4_deg	20.242
r_dihedral_angle_3_deg	13.529
r_dihedral_angle_1_deg	7.71
r_lrange_it	7.23
r_lrange_other	7.126
r_scangle_it	5.668
r_scangle_other	5.61
r_scbond_it	3.776
r_mcangle_it	3.747
r_mcangle_other	3.747
r_scbond_other	3.727
r_mcbond_it	2.678
r_mcbond_other	2.673
r_angle_refined_deg	1.473
r_angle_other_deg	1.287
r_nbd_other	0.241
r_symmetry_nbd_refined	0.22
r_nbd_refined	0.201
r_symmetry_nbd_other	0.18
r_xyhbond_nbd_refined	0.17
r_nbtor_refined	0.16
r_symmetry_xyhbond_nbd_refined	0.116
r_ncsr_local_group_2	0.1
r_ncsr_local_group_1	0.079
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.059
r_symmetry_xyhbond_nbd_other	0.032
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6639
Nucleic Acid Atoms
Solvent Atoms	507
Heterogen Atoms	137

Software

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