9C6Z | pdb_00009c6z

Crystal structure of Staphylococcal Superantigen-Like protein 11 in complex with FB127

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	50 mM Tris-HCl pH 8.5, 50 mM lithium sulphate, 50 mM sodium sulphate, 30% PEG 400

Crystal Properties
Matthews coefficient	Solvent content
4.26	71.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.37	α = 90
b = 101.37	β = 90
c = 65.23	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	PIXEL	DECTRIS EIGER2 XE 9M		2020-09-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 19-ID	0.979	NSLS-II	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.137	36.4	99.83	0.1858	0.993	9.44	9.8		21715

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	2.14	2.193	99.75		0.926

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	2.137	52.413	21715	1023	99.825	0.203	0.2011	0.2054	0.2363	0.2395	49.034

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]
2.458	1.229		2.458		-7.974

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.94
r_dihedral_angle_6_deg	13.566
r_lrange_other	9.181
r_lrange_it	9.17
r_dihedral_angle_1_deg	7.246
r_scangle_it	7.06
r_scangle_other	7.054
r_dihedral_angle_2_deg	5.245
r_scbond_it	4.699
r_scbond_other	4.644
r_mcangle_it	4.406
r_mcangle_other	4.405
r_mcbond_it	3.068
r_mcbond_other	3.061
r_angle_refined_deg	1.831
r_angle_other_deg	1.305
r_chiral_restr_other	0.375
r_symmetry_xyhbond_nbd_refined	0.243
r_nbd_refined	0.224
r_nbd_other	0.2
r_symmetry_nbd_other	0.192
r_nbtor_refined	0.176
r_xyhbond_nbd_refined	0.173
r_symmetry_nbd_refined	0.147
r_symmetry_nbtor_other	0.091
r_chiral_restr	0.084
r_symmetry_xyhbond_nbd_other	0.028
r_bond_refined_d	0.01
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	1539
Nucleic Acid Atoms
Solvent Atoms	90
Heterogen Atoms	65

Software

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