7D6T | pdb_00007d6t

X-ray structure of Clostridium perfringens sortase C with the C-terminal cell wall sorting 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		298	30% (w/v) PEG 4000, 200mM LiSO4, 100mM Tris-HCl, pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.23	α = 90
b = 62.69	β = 102.58
c = 77.69	γ = 90

Symmetry
Space Group	C 1 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++		2019-10-09	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	1.68	19.02	97.6	0.998	12.56	2.4		43526

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	1.68	1.72			0.839

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	6IXZ	1.68	19.02	41328	2197	97.67	0.15873	0.1554	0.17	0.22033	0.23	RANDOM	28.313

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]
0.09		-0.02	-0.17		0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.912
r_dihedral_angle_3_deg	12.661
r_dihedral_angle_4_deg	10.395
r_dihedral_angle_1_deg	7.378
r_scangle_other	6.07
r_long_range_B_refined	5.872
r_long_range_B_other	5.852
r_rigid_bond_restr	5.572
r_scbond_it	5.316
r_scbond_other	5.314
r_mcangle_it	4.598
r_mcangle_other	4.597
r_mcbond_it	3.944
r_mcbond_other	3.853
r_angle_refined_deg	1.535
r_angle_other_deg	1.313
r_chiral_restr	0.074
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002
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_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2966
Nucleic Acid Atoms
Solvent Atoms	194
Heterogen Atoms

Software

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