7D6P | pdb_00007d6p

X-ray structure of the intermolecular complex of Clostridium perfringens sortase C with the C-terminal cell wall sorting signal motif.

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	298	25% (w/v) PEG 3350, 200mM LiSO4, 100mM Tris-HCl, pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.83	56.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.21	α = 90
b = 104.21	β = 90
c = 44.87	γ = 120

Symmetry
Space Group	P 32 2 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	IMAGE PLATE	RIGAKU RAXIS IV++		2019-12-26	M	SINGLE WAVELENGTH

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

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	2.38	18.8	98.6	0.997	11.7	10.5		11342

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	2.38	2.44			0.909

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6IXZ	2.38	18.8	11334	541	98.625	0.246	0.2445	0.25	0.2763	0.28	74.757

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]
-0.013	-0.006		-0.013		0.042

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.156
r_dihedral_angle_3_deg	13.824
r_lrange_other	10.665
r_lrange_it	10.661
r_dihedral_angle_4_deg	8.431
r_dihedral_angle_1_deg	8.088
r_mcangle_other	7.147
r_mcangle_it	7.145
r_scangle_it	6.791
r_scangle_other	6.788
r_mcbond_it	4.534
r_mcbond_other	4.508
r_scbond_it	4.346
r_scbond_other	4.344
r_angle_refined_deg	1.5
r_angle_other_deg	1.09
r_nbtor_refined	0.274
r_symmetry_nbtor_other	0.201
r_symmetry_xyhbond_nbd_refined	0.196
r_nbd_refined	0.162
r_nbd_other	0.16
r_symmetry_nbd_other	0.155
r_xyhbond_nbd_refined	0.151
r_symmetry_nbd_refined	0.134
r_chiral_restr	0.051
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1555
Nucleic Acid Atoms
Solvent Atoms	14
Heterogen Atoms	11

Software

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