8GUU | pdb_00008guu

Crystal structure of pilus-specific sortase C mutant from Streptococcus sanguinis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8GR6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	295	100 mM Sodium Acetate pH 5.5, 200 mM Ammonium sulphate, and 10 % PEG 2000MME.

Crystal Properties
Matthews coefficient	Solvent content
4.52	69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 139.455	α = 90
b = 139.455	β = 90
c = 104.692	γ = 120

Symmetry
Space Group	H 3 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		2020-10-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.97242	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.008	69.82	93.3	0.088	0.026	0.999	15.9	11.8		24438			42.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.008	2.043			1.039	0.348	0.871	2.2	9.9

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	8GR6	2.008	69.82	23165	1269	93.33	0.1848	0.1832	0.1944	0.21408	0.2191	RANDOM	54.637

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]
-1.89	-0.94		-1.89		6.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.147
r_dihedral_angle_3_deg	12.261
r_long_range_B_other	11.861
r_long_range_B_refined	11.844
r_scangle_other	10.992
r_dihedral_angle_4_deg	9.664
r_scbond_it	9.645
r_scbond_other	9.641
r_mcangle_it	6.68
r_mcangle_other	6.68
r_mcbond_it	6.015
r_mcbond_other	5.951
r_dihedral_angle_1_deg	5.585
r_angle_refined_deg	1.068
r_angle_other_deg	0.928
r_chiral_restr	0.058
r_bond_refined_d	0.004
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1523
Nucleic Acid Atoms
Solvent Atoms	87
Heterogen Atoms	8

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing