2AYV | pdb_00002ayv

Crystal structure of a putative ubiquitin-conjugating enzyme E2 from Toxoplasma gondii

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1X23

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	291	3.5M sodium formate, 0.1M sodium acetate, pH 4.6, vapor diffusion, sitting drop, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.7	53.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.553	α = 90
b = 85.611	β = 90
c = 89.612	γ = 90

Symmetry
Space Group	I 2 2 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	IMAGE PLATE	RIGAKU RAXIS		2005-09-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E	1.5418

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	20	99.2	0.038		5.7		12360

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	2.15		96.2	0.331		5.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1X23	2.001	20	12359	597	99.333	0.228	0.2261	0.3004	0.258	0.2921	RANDOM	20.822

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]
1.984			0.39		-2.374

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.319
r_dihedral_angle_3_deg	14.402
r_dihedral_angle_4_deg	8.024
r_dihedral_angle_1_deg	6.15
r_scangle_it	3.666
r_mcangle_it	3.303
r_scbond_it	2.869
r_mcbond_it	2.453
r_angle_refined_deg	1.408
r_nbtor_refined	0.305
r_symmetry_vdw_refined	0.296
r_symmetry_hbond_refined	0.212
r_nbd_refined	0.181
r_xyhbond_nbd_refined	0.141
r_chiral_restr	0.091
r_bond_refined_d	0.016
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1132
Nucleic Acid Atoms
Solvent Atoms	16
Heterogen Atoms	10

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction