3IBZ | pdb_00003ibz

Crystal structure of putative tellurium resistant like protein (TerD) from Streptomyces coelicolor A3(2)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.5	293	0.1M TRIS PH8.5, 12% GLYCEROL, 1.5M NH4SO4, VAPOR DIFFUSION - SITTING DROP, TEMPERATURE 273K, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.836	α = 90
b = 61.456	β = 90
c = 85.713	γ = 90

Symmetry
Space Group	P 21 21 21

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	MIRROR	2009-06-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9793	APS	19-ID

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	1.78	49.94	99.1	0.071	0.071	22.1	3.3		18188		-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	1.78	1.81	100		0.554	0.554	2.2

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 (All)	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	1.78	49.94	18123	18123	929	98.98	0.164	0.164	0.163	0.2	0.2	0.23	RANDOM	7.48

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]
-1.8			-0.28		2.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.288
r_dihedral_angle_4_deg	23.35
r_dihedral_angle_3_deg	14.327
r_dihedral_angle_1_deg	6.421
r_scangle_it	5.398
r_scbond_it	3.348
r_angle_other_deg	2.349
r_mcangle_it	2.191
r_angle_refined_deg	1.789
r_mcbond_it	1.219
r_mcbond_other	0.189
r_chiral_restr	0.12
r_bond_refined_d	0.02
r_gen_planes_refined	0.008
r_gen_planes_other	0.006
r_bond_other_d	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1349
Nucleic Acid Atoms
Solvent Atoms	126
Heterogen Atoms	17

Software

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