3HD0

Crystal structure of Tm1865, an Endonuclease V from Thermotoga Maritima

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	298	Crystallization drop was 1:1 mixture of protein dissolved in 20 mM Tris pH 8.5, 100 mM NaCl and 24 w/v% PEG 1500, 20% glycerol. The crystallization reservoir was 1.5 M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.84	33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.571	α = 90
b = 71.966	β = 90
c = 120.266	γ = 90

Symmetry
Space Group	P 21 21 21

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	MARMOSAIC 300 mm CCD		2007-06-27	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.97876, 0.97860, 0.97243	APS	22-ID

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	2.7	50	99.8	0.131	15.333	5.3		17147

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.7	2.8	99.8		0.453	3.27	4.9

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.7	50	16183	890	99.77	0.16742	0.16275	0.25518	RANDOM	28.281

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]
-0.38			0.75		-0.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.169
r_dihedral_angle_3_deg	19.993
r_dihedral_angle_4_deg	18.132
r_scangle_it	6.646
r_dihedral_angle_1_deg	6.182
r_scbond_it	4.025
r_mcangle_it	2.583
r_angle_refined_deg	1.635
r_mcbond_it	1.491
r_nbtor_refined	0.326
r_nbd_refined	0.234
r_symmetry_vdw_refined	0.214
r_symmetry_hbond_refined	0.187
r_xyhbond_nbd_refined	0.162
r_chiral_restr	0.106
r_bond_refined_d	0.015
r_gen_planes_refined	0.005
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_refined
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	5291
Nucleic Acid Atoms
Solvent Atoms	221
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction