2O0Y | pdb_00002o0y

Crystal structure of putative transcriptional regulator RHA1_ro06953 (IclR-family) from Rhodococcus sp.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	PEG3350 25%, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.247	α = 74.88
b = 69.027	β = 71.47
c = 79.214	γ = 68.87

Symmetry
Space Group	P 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	SBC-3	mirrors	2006-06-11	M	SAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.97904	APS	19-BM

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	50	97.3	0.053	0.042	36	4	75273	73258		-3

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	2.07	91.1		0.244	0.228	6.6	3.7	6874

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	2	36.25	69510	69510	3697	100	0.18482	0.18224	0.18	0.23384	0.23	RANDOM	30.931

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]
-0.05	0.44	0.11	-1.01	-0.07	0.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.744
r_dihedral_angle_4_deg	19.321
r_dihedral_angle_3_deg	14.08
r_dihedral_angle_1_deg	6.133
r_scangle_it	4.04
r_scbond_it	2.926
r_angle_refined_deg	1.617
r_mcangle_it	1.541
r_mcbond_it	1.335
r_nbtor_refined	0.307
r_nbd_refined	0.215
r_symmetry_vdw_refined	0.174
r_xyhbond_nbd_refined	0.168
r_symmetry_hbond_refined	0.16
r_chiral_restr	0.118
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7357
Nucleic Acid Atoms
Solvent Atoms	480
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-3000	phasing
RESOLVE	model building
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing
SHELXE	model building
DM	phasing
MLPHARE	phasing
RESOLVE	phasing
ARP/wARP	model building
O	model building
Coot	model building
CCP4	phasing