1VK2 | pdb_00001vk2

Crystal structure of Uracil-DNA glycosylase (TM0511) from Thermotoga maritima at 1.90 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	8.5	277	TRIS pH 8.5, 8% PEG-8000, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K. cryo condition: 25% PEG-200.

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.049	α = 90
b = 61.049	β = 90
c = 127.5	γ = 90

Symmetry
Space Group	P 43 21 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	ADSC		2004-03-03	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1	1.0000, 0.9796, 0.9794	ALS	8.2.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.9	50	99.97	0.068	25.15	7.87		19816			37.82

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.97	99.95		0.841	2.03	6.13	1938

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	MAD	THROUGHOUT	1.9	44.09	18702	1013	99.96	0.17886	0.17743	0.19	0.20573	0.21	RANDOM	25.426

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]
1.31			1.31		-2.62

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	9.483
r_scbond_it	6.419
r_dihedral_angle_1_deg	5.693
r_mcangle_it	3.691
r_mcbond_it	2.039
r_angle_refined_deg	1.671
r_angle_other_deg	0.867
r_symmetry_vdw_other	0.353
r_nbd_other	0.239
r_nbd_refined	0.208
r_xyhbond_nbd_refined	0.146
r_symmetry_hbond_refined	0.095
r_chiral_restr	0.091
r_nbtor_other	0.084
r_symmetry_vdw_refined	0.044
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_gen_planes_other	0.007
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1479
Nucleic Acid Atoms
Solvent Atoms	114
Heterogen Atoms	11

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
autoSHARP	phasing
REFMAC	refinement