5X86

Crystal structure of TMP bound thymidylate kinase from thermus thermophilus HB8

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		295	0.2M MgCl2.6H2O, 0.1 M Tris hydrochloride, 30% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
1.92	35.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.901	α = 90
b = 47.435	β = 90
c = 152.062	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 225 mm CCD		2014-09-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.8265	ESRF	BM14

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	1.19	50.01	99	1.8	5.7		108625

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	1.19	1.21

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	5X7J	1.19	50.01	103154	5368	99.07	0.14183	0.14053	0.1679	RANDOM	14.304

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]
-0.57			0.29		0.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.269
r_sphericity_free	21.435
r_dihedral_angle_4_deg	19.932
r_dihedral_angle_3_deg	12.205
r_sphericity_bonded	9.991
r_dihedral_angle_1_deg	5.291
r_long_range_B_refined	3.297
r_long_range_B_other	3.098
r_scangle_other	2.819
r_scbond_it	2.296
r_scbond_other	2.285
r_mcangle_it	2.002
r_mcangle_other	2.002
r_angle_refined_deg	1.934
r_rigid_bond_restr	1.761
r_mcbond_it	1.515
r_mcbond_other	1.503
r_angle_other_deg	1.03
r_chiral_restr	0.113
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2907
Nucleic Acid Atoms
Solvent Atoms	315
Heterogen Atoms	52

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing