2ZI8 | pdb_00002zi8

Crystal structure of the HsaC extradiol dioxygenase from M. tuberculosis in complex with 3,4-dihydroxy-9,10-seconandrost-1,3,5(10)-triene-9,17-dione (DHSA)

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	291	12-15% PEG 3350, 0.2M ammonium tartrate, 25% ethylene glycol, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.06	59.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 124.318	α = 90
b = 124.318	β = 90
c = 106.383	γ = 90

Symmetry
Space Group	P 4 21 2

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 315	MC	2007-02-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	1.000	ALS	8.2.2

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	2.2	30	100	0.081	0.081	26		56012	55996	1	1

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)
	2.2	2.32	100		0.389	0.389	6.1		6156

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	1HAN	2.2	20	40622	40622	2156	99.94	0.19738	0.19388	0.2	0.2643	0.26	RANDOM	25.477

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]
-0.83			-0.83		1.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.526
r_dihedral_angle_4_deg	20.966
r_dihedral_angle_3_deg	20.173
r_dihedral_angle_1_deg	11.579
r_scangle_it	4.826
r_scbond_it	3.375
r_angle_refined_deg	2.447
r_mcangle_it	2.082
r_mcbond_it	1.354
r_nbtor_refined	0.307

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.526
r_dihedral_angle_4_deg	20.966
r_dihedral_angle_3_deg	20.173
r_dihedral_angle_1_deg	11.579
r_scangle_it	4.826
r_scbond_it	3.375
r_angle_refined_deg	2.447
r_mcangle_it	2.082
r_mcbond_it	1.354
r_nbtor_refined	0.307
r_metal_ion_refined	0.274
r_nbd_refined	0.268
r_chiral_restr	0.237
r_symmetry_vdw_refined	0.234
r_xyhbond_nbd_refined	0.229
r_symmetry_hbond_refined	0.187
r_bond_refined_d	0.024
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4704
Nucleic Acid Atoms
Solvent Atoms	484
Heterogen Atoms	48

Software

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

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.