7CG9 | pdb_00007cg9

Crystal structure of pilin-specific sortase SrtC1 from Lactobacillus rhamnosus GG

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4G1H

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	295	0.2 M Lithium sulfate, 0.1 M Tris-Cl pH 8.0, 30% (w/v) PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
1.89	34.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.071	α = 90
b = 43.071	β = 90
c = 222.199	γ = 90

Symmetry
Space Group	P 41 21 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		2019-02-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	0.97800	ELETTRA	11.2C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.05	42.32	91	0.062	0.065	0.018	0.93	31	21.9		12848			42.5

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	2.05	2.16	70.5		0.83	0.89	0.29	0.81	3.1	15.3

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	4G1H	2.05	42.32	12165	593	91.1	0.23499	0.2345	0.25	0.24435	0.26	RANDOM	46.765

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]
1.28			1.28		-2.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.533
r_dihedral_angle_3_deg	14.274
r_dihedral_angle_4_deg	9.387
r_long_range_B_refined	8.7
r_long_range_B_other	8.7
r_dihedral_angle_1_deg	7.59
r_scangle_other	7.044
r_mcangle_it	5.034
r_mcangle_other	5.031
r_scbond_it	4.952
r_scbond_other	4.937
r_mcbond_it	3.379
r_mcbond_other	3.378
r_angle_other_deg	2.328
r_angle_refined_deg	1.469
r_chiral_restr	0.061
r_bond_other_d	0.036
r_gen_planes_other	0.009
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
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	1469
Nucleic Acid Atoms
Solvent Atoms	26
Heterogen Atoms	10

Software

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