8QTY

LytR LCP domain from Streptococcus dysgalactiae subs. dysgalactiae

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3OKZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		292	2.2 M ammonium sulphate 20% glycerol

Crystal Properties
Matthews coefficient	Solvent content
4.96	75.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 141.271	α = 90
b = 141.271	β = 90
c = 133.742	γ = 90

Symmetry
Space Group	I 4 2 2

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		2016-07-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.966	ESRF	MASSIF-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.8	48.608	99.9	0.999	15.5	8		16955

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	2.8	2.95			0.666

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.8	48.608	16955	895	99.776	0.272	0.2714	0.2927	80.154

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]
-0.932			-0.932		1.865

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	24.182
r_dihedral_angle_2_deg	18.605
r_dihedral_angle_6_deg	16.352
r_lrange_it	6.437
r_lrange_other	6.437
r_dihedral_angle_1_deg	6.143
r_mcangle_it	5.689
r_mcangle_other	5.687
r_scangle_other	4.5
r_scangle_it	4.475
r_mcbond_it	4.044
r_mcbond_other	4.044
r_scbond_other	2.678
r_scbond_it	2.661
r_angle_refined_deg	1.968
r_symmetry_nbd_refined	0.722
r_symmetry_xyhbond_nbd_refined	0.691
r_angle_other_deg	0.623
r_nbd_other	0.517
r_nbd_refined	0.249
r_symmetry_nbd_other	0.225
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.133
r_chiral_restr	0.089
r_symmetry_nbtor_other	0.084
r_bond_refined_d	0.017
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_ext_dist_refined_b

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2076
Nucleic Acid Atoms
Solvent Atoms	25
Heterogen Atoms	15

Software

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