2F4Z | pdb_00002f4z

Toxoplasma gondii ubiquitin conjugating enzyme TgTwinScan_2721- E2 domain

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BEP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.4	297	32% Peg 1500, 0.2 M MgCl2, 0.1 M Tris pH 8.4, 10 mM Spermidine, VAPOR DIFFUSION, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.475	α = 90
b = 141.334	β = 90
c = 77.13	γ = 90

Symmetry
Space Group	C 2 2 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	IMAGE PLATE	RIGAKU RAXIS IV	VeriMax	2005-09-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E	1.54

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	2.12	50	98.8	0.077	0.077	7.6	6.3	23386	23386			36.3

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	2.12	2.16	97.3		0.729	0.729	2.22	6.3	1143

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 (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	MOLECULAR REPLACEMENT	THROUGHOUT	2BEP	2.11	50	22605	22605	763	98.66	0.19992	0.19992	0.1987	0.2	0.23779	0.2	RANDOM	35.401

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]
1.22			-0.73		-0.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.176
r_dihedral_angle_4_deg	27.115
r_dihedral_angle_3_deg	16.543
r_dihedral_angle_1_deg	6.386
r_scangle_it	4.977
r_scbond_it	3.206
r_mcangle_it	2.137
r_angle_refined_deg	1.892
r_mcbond_it	1.339
r_nbtor_refined	0.315
r_symmetry_hbond_refined	0.271
r_xyhbond_nbd_refined	0.255
r_nbd_refined	0.221
r_symmetry_vdw_refined	0.15
r_chiral_restr	0.129
r_bond_refined_d	0.02
r_gen_planes_refined	0.009
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	2259
Nucleic Acid Atoms
Solvent Atoms	194
Heterogen Atoms	7

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
HKL-2000	data scaling
PHASER	phasing
Coot	model building