7QXD | pdb_00007qxd

Recognition of Staphylococcus aureus wall teichoic acid analogue SA475 (compound 2) 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		294	10 mM 2-(N-morpholino)ethanesulfonic acid-NaOH pH 6.2, 0.25 M sodium chloride, 20% (w/v) poly-ethylene glycol 4000, 10% (v/v) glycerol, 200 mM magnesium sulphate

Crystal Properties
Matthews coefficient	Solvent content
3	59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.392	α = 90
b = 113.371	β = 90
c = 154.557	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		2020-06-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.97933	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	1.649	91.41	92.9	0.077	0.092	0.049	0.998	12	6.5		127285			24.4

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	1.649	1.74	100		1.047	1.247	0.67	0.661	1.5	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	1.649	90.016	127097	6287	92.962	0.176	0.1747	0.19	0.2018	0.21	25.699

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			-0.59		-0.157

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.184
r_dihedral_angle_4_deg	22.83
r_dihedral_angle_3_deg	13.049
r_dihedral_angle_1_deg	7.67
r_lrange_it	6.64
r_lrange_other	6.503
r_scangle_it	4.859
r_scangle_other	4.832
r_mcangle_it	3.239
r_mcangle_other	3.238
r_scbond_it	3.15
r_scbond_other	3.123
r_mcbond_it	2.166
r_mcbond_other	2.161
r_angle_refined_deg	1.548
r_angle_other_deg	1.394
r_symmetry_nbd_refined	0.231
r_symmetry_xyhbond_nbd_other	0.212
r_nbd_refined	0.196
r_symmetry_nbd_other	0.18
r_nbd_other	0.18
r_symmetry_xyhbond_nbd_refined	0.175
r_xyhbond_nbd_refined	0.174
r_nbtor_refined	0.164
r_ncsr_local_group_1	0.092
r_ncsr_local_group_2	0.091
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.069
r_bond_refined_d	0.01
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	6636
Nucleic Acid Atoms
Solvent Atoms	818
Heterogen Atoms	125

Software

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