6Q2L | pdb_00006q2l

The structure of the Streptococcus gordonii surface protein SspB in complex with TEV peptide provides clues to the adherence of oral streptococcal adherence to salivary agglutinin

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6Q2K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	20-25% PEG 8000, 0.1M succinic acid, pH 5.0-5.5, 100mM MgCl2

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.223	α = 90
b = 47.695	β = 113.6
c = 64.652	γ = 90

Symmetry
Space Group	P 1 21 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 PILATUS 200K	Osmic Mirrors	2017-05-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.8	50	98.9	0.084	0.097	0.047	11.8	3.3		31075			17.4

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	1.8	1.83	83.9		0.419	0.567	0.38	0.714	1.6	1.5

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6Q2K	1.8	37.15	29507	1554	98.81	0.197	0.195	0.2	0.232	0.23	RANDOM	22.5

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]
0.02		0.02	-0.08		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.396
r_dihedral_angle_4_deg	15.989
r_dihedral_angle_3_deg	12.415
r_dihedral_angle_1_deg	6.762
r_angle_refined_deg	1.299
r_angle_other_deg	0.882
r_chiral_restr	0.077
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2345
Nucleic Acid Atoms
Solvent Atoms	351
Heterogen Atoms	7

Software

Software
Software Name	Purpose
HKL-2000	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction