3EBM

Crystal structure of human translationally controlled tumour associated protein (hTCTP) mutant E12V

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1YZ1	PDB ENTRY 1YZ1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.2	277	0.1M Tris, pH 8.2, 22% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.192	α = 90
b = 81.543	β = 90
c = 139.92	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 210		2008-05-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.0000	Photon Factory	AR-NW12A

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	2.6	50	97.5	0.096	0.096	13.6	4	28188	27483

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)
	2.6	2.69	97.5		0.467	0.467	2.9	3.7

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1YZ1	2.6	36	26812	26115	1366	97.4	0.23883	0.23883	0.23657	0.28031	RANDOM	55.88

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]
-2.24			7.4		-5.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.026
r_dihedral_angle_4_deg	18.239
r_dihedral_angle_3_deg	15.131
r_scangle_it	6.503
r_dihedral_angle_1_deg	4.505
r_mcangle_it	4.263
r_scbond_it	4.078
r_rigid_bond_restr	3.453
r_mcbond_it	3.118
r_sphericity_free	1.227
r_sphericity_bonded	1.004
r_angle_refined_deg	0.897
r_nbtor_refined	0.298
r_symmetry_vdw_refined	0.228
r_nbd_refined	0.193
r_symmetry_hbond_refined	0.175
r_xyhbond_nbd_refined	0.124
r_chiral_restr	0.068
r_bond_refined_d	0.009
r_gen_planes_refined	0.002
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4788
Nucleic Acid Atoms
Solvent Atoms	37
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling