8WG6 | pdb_00008wg6

Crystal structure of major pilin PilB from Streptococcus sanguinis - SeMet derivative

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	295	0.2 M Potassium acetate, 0.1 M Hepes pH 7.0, 5% w/v polyvinyl alcohol.

Crystal Properties
Matthews coefficient	Solvent content
2.4	48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.78	α = 90
b = 58.772	β = 90
c = 214.108	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		2019-09-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	0.9803	ELETTRA	11.2C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.399	56.677	98.2	0.054	0.997	15.7	46.5		19213

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.399	2.447	86.3		0.265	0.918	3.5	46.8

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	FREE R-VALUE	2.4	45.41	18274	934	98.21	0.22828	0.22615	0.2379	0.26939	0.2802	RANDOM	18.328

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]
-0.93			-0.18		1.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	11.996
r_dihedral_angle_1_deg	6.909
r_dihedral_angle_2_deg	5.29
r_long_range_B_refined	3.296
r_long_range_B_other	3.23
r_scangle_other	1.365
r_mcangle_it	0.986
r_mcangle_other	0.986
r_angle_refined_deg	0.973
r_scbond_it	0.772
r_scbond_other	0.771
r_mcbond_it	0.596
r_mcbond_other	0.554
r_angle_other_deg	0.315
r_chiral_restr	0.038
r_bond_refined_d	0.005
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3176
Nucleic Acid Atoms
Solvent Atoms	146
Heterogen Atoms	13

Software

Software
Software Name	Purpose
XDS	data reduction
CRANK2	phasing
Coot	model building
REFMAC	refinement
autoPROC	data reduction