4QGL | pdb_00004qgl

Acireductone dioxygenase from Bacillus anthracis with three cadmium ions

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VR3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9	289	Protein: 5.5mg/ml, in 50 mM Tris-HCl pH 7.8, 150mM NaCl, 1mM CdCl2, Crystallization condition: 62% Tacsimate pH=9.0, 15mM NaCl, 2% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.761	α = 90
b = 57.69	β = 98.15
c = 33.98	γ = 90

Symmetry
Space Group	C 1 2 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	CCD	MARMOSAIC 300 mm CCD	Beryllium Lenses	2012-04-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97857	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.6	50	85.6	0.111	0.111	11.987	2.3	5354	5354		-3	40.41

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.64	85.6		0.511	0.511	2.39	2.2	250

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	1vr3	2.61	19.85	5103	5103	251	84.74	0.17848	0.17605	0.1671	0.2257	0.2163	RANDOM	30.418

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]
1.14		7.51	-26.62		25.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.598
r_dihedral_angle_3_deg	17.967
r_dihedral_angle_4_deg	16.497
r_dihedral_angle_1_deg	7.15
r_angle_refined_deg	1.539
r_angle_other_deg	0.845
r_chiral_restr	0.087
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1399
Nucleic Acid Atoms
Solvent Atoms	32
Heterogen Atoms	3

Software

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