1YD3 | pdb_00001yd3

Crystal structure of the GIY-YIG N-terminal endonuclease domain of UvrC from Thermotoga maritima: Point mutant Y43F bound to its catalytic divalent cation

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 = 56.094	α = 90
b = 56.094	β = 90
c = 111.491	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	1.6	30	99.2			44684	44684	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	1.6	1.64	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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	1.6	15	2	22868	22868	1220	99.53	0.18	0.1755	0.17457	0.19	0.19381	RANDOM	20.212

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]
0.27			0.27		-0.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.532
r_dihedral_angle_4_deg	18.583
r_dihedral_angle_3_deg	12.148
r_sphericity_free	5.573
r_dihedral_angle_1_deg	5.233
r_scangle_it	4.227
r_rigid_bond_restr	3.435
r_scbond_it	3.176
r_sphericity_bonded	2.723
r_mcangle_it	1.9
r_mcbond_it	1.768
r_angle_refined_deg	1.369
r_angle_other_deg	0.913
r_mcbond_other	0.515
r_symmetry_vdw_other	0.323
r_nbd_refined	0.216
r_nbtor_refined	0.156
r_nbd_other	0.154
r_symmetry_vdw_refined	0.147
r_symmetry_hbond_refined	0.146
r_xyhbond_nbd_refined	0.135
r_chiral_restr	0.088
r_nbtor_other	0.07
r_bond_refined_d	0.018
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	748
Nucleic Acid Atoms
Solvent Atoms	173
Heterogen Atoms	11

Software

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