3T8L

Crystal Structure of adenine deaminase with Mn/Fe

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3NQB	PDB entry 3NQB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	298	0.2M Magnesium chloride hexahydrate, 0.1M HEPES 7.5, 25% (w/v) PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.543	α = 90
b = 131.171	β = 97.04
c = 69.284	γ = 90

Symmetry
Space Group	P 1 21 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	ADSC QUANTUM 315	mirrors	2010-11-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.979	NSLS	X29A

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	2.8	50	99.7	0.175			26874	26874

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.85	97

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	Difference Fourier	THROUGHOUT	PDB entry 3NQB	2.8	48.73	25427	25427	1362	99.69	0.18058	0.17418	0.30067	RANDOM	49.749

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]
0.03		-0.02	-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.129
r_dihedral_angle_3_deg	22.896
r_dihedral_angle_4_deg	21.617
r_dihedral_angle_1_deg	9.708
r_scangle_it	6.863
r_scbond_it	4.98
r_angle_refined_deg	3.398
r_mcangle_it	2.752
r_mcbond_it	2.058
r_nbtor_refined	0.348
r_nbd_refined	0.29
r_symmetry_vdw_refined	0.264
r_chiral_restr	0.207
r_xyhbond_nbd_refined	0.198
r_symmetry_hbond_refined	0.153
r_metal_ion_refined	0.098
r_bond_refined_d	0.048
r_gen_planes_refined	0.013
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_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	8672
Nucleic Acid Atoms
Solvent Atoms	83
Heterogen Atoms	6

Software

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