1YD1

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

X-RAY DIFFRACTION

---

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 = 55.246	α = 90
b = 55.246	β = 90
c = 108.63	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	1.8	30	99.7			16305	16305	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	1.8	1.86	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	1.8	15	2	15386	15386	830	99.78	0.18	0.17647	0.17518	0.20198	RANDOM	21.77

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]
0.26			0.26		-0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.169
r_dihedral_angle_4_deg	16.922
r_dihedral_angle_3_deg	14.126
r_dihedral_angle_1_deg	5.154
r_scangle_it	5.135
r_scbond_it	3.487
r_mcangle_it	1.641
r_mcbond_it	1.585
r_angle_refined_deg	1.473
r_symmetry_metal_ion_refined	1.112
r_angle_other_deg	0.821
r_symmetry_vdw_other	0.306
r_mcbond_other	0.292
r_nbd_refined	0.226
r_nbtor_refined	0.182
r_nbd_other	0.173
r_symmetry_hbond_refined	0.128
r_symmetry_vdw_refined	0.113
r_xyhbond_nbd_refined	0.112
r_nbtor_other	0.084
r_chiral_restr	0.083
r_bond_refined_d	0.017
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	738
Nucleic Acid Atoms
Solvent Atoms	96
Heterogen Atoms	8

Software

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