2W04

Co-complex Structure of Achromobactin Synthetase Protein D (AcsD) with citrate in ATP binding site from Pectobacterium Chrysanthemi

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		APO STRUCTURE OF ACSD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.8		26%PEG8000, 0.1M TRIS-HCL PH7.8, 300MM SODIUM CITRATE ACSD WAS INCUBATED WITH 2 MM ATP-GAMMA-S (SIGMA A1388) FOR 10 MIN (RT). 3UL ACSD (6MG/ML) AND EQUAL AMOUNT OF PRECIPITANT WERE INCUBATED IN CONVENTIONAL HANGING DROP PLATES.

Crystal Properties
Matthews coefficient	Solvent content
2.15	43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.371	α = 90
b = 94.959	β = 90
c = 160.261	γ = 90

Symmetry
Space Group	P 21 21 21

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	MARRESEARCH	SINGLE SILICON (111) MONOCHROMATOR	2007-04-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1		ESRF	ID23-1

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	2.8	81.6	99.4	0.16	10.6	4.2		30736		2

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	2.8	2.95	99.9		0.41	3	4.3

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	APO STRUCTURE OF ACSD	2.8	81.65	29085	1513	98.9	0.206	0.202	0.21	0.28	0.28	RANDOM	11.74

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]
-1.53			-1.78		3.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.559
r_dihedral_angle_3_deg	18.007
r_dihedral_angle_4_deg	17.691
r_dihedral_angle_1_deg	6.4
r_scangle_it	1.823
r_angle_refined_deg	1.461
r_scbond_it	1.096
r_mcangle_it	0.783
r_mcbond_it	0.451
r_nbtor_refined	0.31
r_symmetry_vdw_refined	0.252
r_symmetry_hbond_refined	0.252
r_nbd_refined	0.229
r_xyhbond_nbd_refined	0.171
r_chiral_restr	0.099
r_bond_refined_d	0.013
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9215
Nucleic Acid Atoms
Solvent Atoms	130
Heterogen Atoms	13

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing