9C65 | pdb_00009c65

Crystal structure of Staphylococcal Superantigen-Like protein 11 in complex with SB618

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2RDG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	100 mM HEPES/NaOH pH 7.0, 55% MPD

Crystal Properties
Matthews coefficient	Solvent content
4.31	71.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.464	α = 90
b = 104.464	β = 90
c = 62.136	γ = 120

Symmetry
Space Group	P 31 2 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	CCD	RIGAKU SATURN 944	Rigaku	2023-10-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.458	13.813	97.89	0.2502	0.06434	0.996	12.51	9.9		14193			44.13

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.458	2.52	92.21		0.507	1.6

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	2.458	13.813	14193	658	97.613	0.175	0.1738	0.1819	0.2077	0.2073	53.223

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]
-0.332	-0.166		-0.332		1.077

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.974
r_dihedral_angle_6_deg	14.771
r_lrange_it	14.371
r_lrange_other	14.371
r_scangle_it	10.214
r_scangle_other	10.212
r_dihedral_angle_2_deg	10.148
r_mcangle_other	8.127
r_mcangle_it	8.126
r_dihedral_angle_1_deg	8.019
r_scbond_it	6.941
r_scbond_other	6.937
r_mcbond_it	5.43
r_mcbond_other	5.425
r_angle_refined_deg	2.672
r_angle_other_deg	0.926
r_nbd_refined	0.269
r_nbd_other	0.25
r_symmetry_nbd_refined	0.248
r_symmetry_xyhbond_nbd_refined	0.244
r_symmetry_nbd_other	0.215
r_nbtor_refined	0.193
r_xyhbond_nbd_refined	0.166
r_chiral_restr	0.134
r_symmetry_nbtor_other	0.102
r_chiral_restr_other	0.044
r_bond_refined_d	0.016
r_gen_planes_refined	0.012
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1490
Nucleic Acid Atoms
Solvent Atoms	103
Heterogen Atoms	58

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
Coot	model building
PHASER	phasing