4JB7 | pdb_00004jb7

1.42 Angstrom resolution crystal structure of accessory colonization factor AcfC (acfC) in complex with D-aspartic acid

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9	295	Protein: 7.3 mg/mL in 10 mM Tris-HCl, pH 8.0, 0.25 M NaCl 5 mM BME. Crystallization: PACT Suite D6(#42): 0.1 M MMT buffer pH 9.0 25 % (w/v) PEG1500, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.343	α = 90
b = 72.343	β = 90
c = 87.883	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	CCD	MARMOSAIC 300 mm CCD	Be-Lenses	2013-02-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

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	1.42	30	100	0.087	45.47	9.5	44772	44772		-3

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	1.42	1.44	100		0.615	3.82	9.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	1.42	27.93	42343	42343	2249	99.95	0.12667	0.12589	0.1251	0.14148	0.1402	RANDOM	14.643

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]
-0.03			-0.03		0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.762
r_dihedral_angle_4_deg	15.747
r_dihedral_angle_3_deg	10.721
r_dihedral_angle_1_deg	4.646
r_scangle_it	4.06
r_scbond_it	2.635
r_mcangle_it	1.705
r_angle_refined_deg	1.489
r_mcbond_it	1.036
r_angle_other_deg	0.94
r_mcbond_other	0.37
r_chiral_restr	0.099
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1827
Nucleic Acid Atoms
Solvent Atoms	365
Heterogen Atoms	37

Software

Software
Software Name	Purpose
Blu-Ice	data collection
MLPHARE	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling