4QGM | pdb_00004qgm

Acireductone dioxygenase from Bacillus anthracis with cadmium ion in active center

X-RAY DIFFRACTION

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 CdCl, Crystallization condition: 62% Tacsimate pH=9.0, 0.0075M CdCl2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.215	α = 90
b = 49.522	β = 99.95
c = 33.349	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 225 mm CCD	Beryllium Lenses	2012-03-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.9787	APS	21-ID-F

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	3	50	99.9	0.112	0.112	11.046	3.7	3560	3560		-3	57.37

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	3	3.05	100		0.473	0.473	2.919	3.7	179

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	2.97	52.31	3386	3386	152	97.57	0.1861	0.18386	0.19	0.23423	0.25	RANDOM	37.763

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]
-2.22		-0.35	0.1		2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.304
r_dihedral_angle_3_deg	16.48
r_dihedral_angle_4_deg	12.79
r_dihedral_angle_1_deg	7.661
r_angle_refined_deg	1.358
r_angle_other_deg	0.866
r_chiral_restr	0.075
r_bond_refined_d	0.01
r_bond_other_d	0.006
r_gen_planes_refined	0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.304
r_dihedral_angle_3_deg	16.48
r_dihedral_angle_4_deg	12.79
r_dihedral_angle_1_deg	7.661
r_angle_refined_deg	1.358
r_angle_other_deg	0.866
r_chiral_restr	0.075
r_bond_refined_d	0.01
r_bond_other_d	0.006
r_gen_planes_refined	0.005
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1353
Nucleic Acid Atoms
Solvent Atoms	14
Heterogen Atoms	1

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.