2J4Q

Crystal structure of a E138A Escherichia coli dCTP deaminase mutant enzyme in complex with dTTP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1XS1	PDB ENTRY 1XS1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.8		VAPOUR DIFFUSION, 34% PEG400, 0.2M MAGNESIUM CHLORIDE, 0.1M HEPES PH6.8, 5MM DCTP

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.594	α = 90
b = 61.594	β = 90
c = 344.766	γ = 120

Symmetry
Space Group	P 63 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	CCD	MARRESEARCH		2003-12-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I911-2		MAX II	I911-2

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	2.6	50	92.7	0.14	21.9	12.2		12085

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	2.6	2.74	70		0.52	2.6	5.5

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1XS1	2.6	30	11438	582	92.6	0.25	0.247	0.302	RANDOM	29.15

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]
2.26	1.13		2.26		-3.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.017
r_dihedral_angle_4_deg	23.781
r_dihedral_angle_3_deg	18.017
r_dihedral_angle_1_deg	7.543
r_scangle_it	2.524
r_angle_refined_deg	1.716
r_scbond_it	1.666
r_mcangle_it	1.22
r_mcbond_it	1.082
r_angle_other_deg	1.027
r_chiral_restr	0.242
r_nbd_refined	0.227
r_symmetry_vdw_refined	0.218
r_symmetry_vdw_other	0.209
r_symmetry_hbond_refined	0.199
r_nbd_other	0.197
r_xyhbond_nbd_refined	0.149
r_nbtor_other	0.089
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2641
Nucleic Acid Atoms
Solvent Atoms	5
Heterogen Atoms	55

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing