5XCB | pdb_00005xcb

X-ray structure of domains D1 and D2 of Clostridium perfringens pili protein CppA

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	0.06M Magnesium chloride hexahydrate, 0.06M Calcium chloride dihydrate, 0.1M Tris (base), 0.1M BICINE, 20% v/v PEG 500* MME, 10 % w/v PEG 20000

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.4	α = 90
b = 141.33	β = 90
c = 61.48	γ = 90

Symmetry
Space Group	C 2 2 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	IMAGE PLATE	RIGAKU RAXIS VII		2016-11-02	M	SINGLE WAVELENGTH

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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.14	18.76	99.7	0.052	22.86	6.5		22094

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.14	2.2	99.8		0.487	4.01

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	MOLECULAR REPLACEMENT	THROUGHOUT	2.14	18.76	20965	1129	99.69	0.21325	0.21123	0.22	0.25123	0.26	RANDOM	47.056

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]
0.01					-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.675
r_dihedral_angle_3_deg	12.997
r_long_range_B_refined	6.413
r_long_range_B_other	6.37
r_dihedral_angle_1_deg	6.269
r_scangle_other	4.156
r_mcangle_it	3.725
r_mcangle_other	3.724
r_dihedral_angle_4_deg	3.216
r_scbond_it	2.623
r_scbond_other	2.623
r_mcbond_it	2.396
r_mcbond_other	2.395
r_angle_refined_deg	1.085
r_angle_other_deg	0.596
r_chiral_restr	0.063
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_bond_other_d
r_gen_planes_other
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	2375
Nucleic Acid Atoms
Solvent Atoms	150
Heterogen Atoms

Software

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