3O82 | pdb_00003o82

Structure of BasE N-terminal domain from Acinetobacter baumannii bound to 5'-O-[N-(2,3-dihydroxybenzoyl)sulfamoyl] adenosine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MDB	PDB ENTRY 1MDB residues 1-430

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	287	5-15% PEG 8000, 5% MPD, 250-600 mM CaCl2, 50 mM BTP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 287K

Crystal Properties
Matthews coefficient	Solvent content
2.91	57.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.447	α = 90
b = 145.259	β = 90
c = 149.063	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	113	CCD	ADSC QUANTUM 315r		2008-02-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-1	0.979	SSRL	BL9-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.7	40	97.5	0.131	9.2	3.8	39977	38979		-3	56.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.7	2.8	81.9		0.377	2.2	3.2

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 1MDB residues 1-430	2.7	40	36904	1966	97.54	0.20285	0.20028	0.2022	0.25128	0.2489	RANDOM	57.064

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]
1.27			1.97		-3.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.508
r_dihedral_angle_4_deg	20.443
r_dihedral_angle_3_deg	17.143
r_dihedral_angle_1_deg	6.435
r_scangle_it	3.828
r_scbond_it	2.261
r_angle_refined_deg	1.732
r_mcangle_it	1.628
r_mcbond_it	0.839
r_chiral_restr	0.111
r_bond_refined_d	0.017
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6762
Nucleic Acid Atoms
Solvent Atoms	49
Heterogen Atoms	70

Software

Software
Software Name	Purpose
Web-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling