1YD4

Crystal structure of the GIY-YIG N-terminal endonuclease domain of UvrC from Thermotoga maritima: Point mutant Y29F bound to its catalytic divalent cation

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	295	PEG 8000, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.7	66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.949	α = 90
b = 54.949	β = 90
c = 109.187	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 QUANTUM 4		2004-01-01	M	SINGLE WAVELENGTH
2	1
3	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X26C	1.1	NSLS	X26C
2	SYNCHROTRON	NSLS BEAMLINE X12B	1.1	NSLS	X12B
3	SYNCHROTRON	NSLS BEAMLINE X25	1.1	NSLS	X25

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	30	100			25177	25177	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.9	1.97	100

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	FOURIER SYNTHESIS	THROUGHOUT	1.9	15	2	13072	13072	693	99.9	0.185	0.17231	0.17064	0.20551	RANDOM	21.86

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]
0.43			0.43		-0.85

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.275
r_dihedral_angle_4_deg	21.767
r_dihedral_angle_3_deg	16.205
r_dihedral_angle_1_deg	5.304
r_scangle_it	5.161
r_scbond_it	3.726
r_mcbond_it	1.671
r_mcangle_it	1.663
r_angle_refined_deg	1.527
r_angle_other_deg	0.842
r_symmetry_vdw_other	0.31
r_mcbond_other	0.29
r_nbd_refined	0.232
r_symmetry_vdw_refined	0.223
r_nbtor_refined	0.185
r_nbd_other	0.183
r_xyhbond_nbd_refined	0.182
r_symmetry_hbond_refined	0.161
r_chiral_restr	0.094
r_nbtor_other	0.089
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	737
Nucleic Acid Atoms
Solvent Atoms	119
Heterogen Atoms	3

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing