2X3J | pdb_00002x3j

CO-COMPLEX STRUCTURE OF ACHROMOBACTIN SYNTHETASE PROTEIN D (ACSD) WITH ATP AND N-CITRYL-ETHYLENEDIAMINE FROM PECTOBACTERIUM CHRYSANTHEMI

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3FFE	PDB ENTRY 3FFE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	FOR CO-CRYSTALLIZATION WITH N-CITRYL-ETHYLENEDIAMINE 9 MG/ML WT ACSD (STORED IN PROTEIN BUFFER: 50 MM TRIS-HCL PH 7.5, 500 MM NACL, 10 % GLYCEROL) WAS INCUBATED FOR ONE HOUR WITH 15 MM ETHYLENEDIAMINE, 10 MM MGCL2, 15 MM ATP AND 15 MM CITRATE. THE SUPERNATANT WAS USED TO GROW N-CITRYL-ETHYLENEDIAMINE CO-COMPLEX CRYSTALS IN HANGING DROPS FROM EQUAL MIXTURES WITH 0.1 M HEPES PH 7.2, 17% PEG 8000, 7.5% (V/V) GLYCEROL AT 20C

Crystal Properties
Matthews coefficient	Solvent content
2.7	55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.704	α = 97.26
b = 71.521	β = 101.97
c = 95.595	γ = 91.01

Symmetry
Space Group	P 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				2008-11-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29		ESRF	ID29

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	50	93.8	0.06	12.8	3.1		89038		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	2.07	74.7		0.35	2.7	2.7

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	PDB ENTRY 3FFE	2	92.85	89038	4680	93.59	0.19204	0.18994	0.19	0.23129	0.23	RANDOM	38.189

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]
-0.72	-3.34	-1.85	2.66	0.92	-2.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.732
r_dihedral_angle_4_deg	17.827
r_dihedral_angle_3_deg	14.308
r_dihedral_angle_1_deg	5.781
r_scangle_it	2.705
r_scbond_it	1.733
r_angle_refined_deg	1.264
r_mcangle_it	1.256
r_mcbond_it	0.75
r_nbtor_refined	0.304
r_symmetry_vdw_refined	0.217
r_nbd_refined	0.203
r_xyhbond_nbd_refined	0.144
r_symmetry_hbond_refined	0.144
r_chiral_restr	0.084
r_bond_refined_d	0.01
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	9323
Nucleic Acid Atoms
Solvent Atoms	571
Heterogen Atoms	110

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing