3C8G | pdb_00003c8g

Crystal structure of a possible transciptional regulator YggD from Shigella flexneri 2a str. 2457T

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	30% (w/v) PEG MME 2000, 0.1M Sodium acetate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.365	α = 90
b = 70.946	β = 90.43
c = 159.037	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	SBC-3	Mirrors	2006-03-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.97883	APS	19-BM

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	2.5	32	94.2	0.074	30.78	4	26162	26162			71.63

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	2.5	2.59	78.9		0.52	1.88	3.2	2140

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	2.5	31.81	24064	24064	2020	93.92	0.21163	0.21163	0.20669	0.2039	0.27034	0.2629	RANDOM	63.751

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]
-0.3		-0.27	0.13		0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.817
r_dihedral_angle_4_deg	23.332
r_dihedral_angle_3_deg	22.759
r_dihedral_angle_1_deg	6.195
r_scangle_it	2.881
r_scbond_it	1.877
r_angle_refined_deg	1.721
r_mcangle_it	1.223
r_mcbond_it	0.739
r_nbtor_refined	0.322
r_symmetry_vdw_refined	0.252
r_nbd_refined	0.246
r_symmetry_hbond_refined	0.171
r_xyhbond_nbd_refined	0.137
r_chiral_restr	0.126
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
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	5334
Nucleic Acid Atoms
Solvent Atoms	12
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELXD	phasing
MLPHARE	phasing
DM	phasing
RESOLVE	phasing
HKL-3000	phasing