4EYE | pdb_00004eye

Crystal structure of a probable oxidoreductase from Mycobacterium abscessus solved by iodide ion SAD

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	289	MyabA.01189.a.A1 PS00933 at 28 mg/mL supplemented with 0.5 M KI against Morpheus screen condition D4, 12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD, 0.1 M MES/imidazole pH 6.5, 0.02 M alcohols, crystal tracking ID 233762d4, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.64	α = 90
b = 46.34	β = 93.14
c = 84.13	γ = 90

Symmetry
Space Group	P 1 21 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	ADSC QUANTUM 315r		2012-04-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	1.5418	SSRL	BL7-1

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	2.1	50	99.8	0.072	17.46	7.1	35785	35731		-3	36.245

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	2.1	2.15	100		0.47	4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	2.1	50	35731	1790	99.79	0.1875	0.185	0.19	0.2345	0.23	RANDOM	32.9471

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]
-0.29		-0.2	-0.05		0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.832
r_dihedral_angle_4_deg	22.106
r_dihedral_angle_3_deg	12.529
r_dihedral_angle_1_deg	6.135
r_angle_refined_deg	1.433
r_angle_other_deg	1.096
r_chiral_restr	0.09
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.832
r_dihedral_angle_4_deg	22.106
r_dihedral_angle_3_deg	12.529
r_dihedral_angle_1_deg	6.135
r_angle_refined_deg	1.433
r_angle_other_deg	1.096
r_chiral_restr	0.09
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.004
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4434
Nucleic Acid Atoms
Solvent Atoms	284
Heterogen Atoms	34

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

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.