6D7Y | pdb_00006d7y

1.75 Angstrom Resolution Crystal Structure of the Toxic C-Terminal Tip of CdiA from Pseudomonas aeruginosa in Complex with Immune Protein

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	292	Protein: 6.4mg/ml, 0.5 Sodium chloride, 0.01M Tris pH 8.3; Screen: Clasics II (D6), 0.1M Bis-Tris pH 5.5, 25% (w/v) PEG 3350;

Crystal Properties
Matthews coefficient	Solvent content
1.85	33.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.579	α = 90
b = 76.579	β = 90
c = 61.441	γ = 120

Symmetry
Space Group	P 63

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD		2017-04-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.75	30	99.9	0.075	0.075	0.082	0.032	30.7	6.6		20855		-3	27.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.78	100		0.799	0.799	0.868	0.34	0.722	2.4	6.6

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	SAD	THROUGHOUT	1.75	29.18	19733	1012	99.91	0.185	0.18302	0.19	0.22364	0.23	RANDOM	37.575

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]
-0.84	-0.42		-0.84		2.73

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.142
r_dihedral_angle_4_deg	13.449
r_dihedral_angle_3_deg	9.372
r_long_range_B_refined	5.219
r_long_range_B_other	5.183
r_scangle_other	3.108
r_dihedral_angle_1_deg	2.871
r_mcangle_other	2.508
r_mcangle_it	2.507
r_scbond_it	1.989
r_scbond_other	1.988
r_mcbond_it	1.536
r_mcbond_other	1.528
r_angle_refined_deg	1.507
r_angle_other_deg	0.88
r_chiral_restr	0.093
r_gen_planes_refined	0.023
r_gen_planes_other	0.019
r_bond_refined_d	0.009
r_bond_other_d	0.001
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	1974
Nucleic Acid Atoms
Solvent Atoms	98
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing