5XAI | pdb_00005xai

dTMP bound Crystal structure of thymidylate kinase (aq_969) from Aquifex Aeolicus VF5

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2PBR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	7.5	293	0.1M HEPES, 10% w/v Polyethylene glycol 8000, 8% v/v Ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
2.46	50.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.634	α = 92.17
b = 52.118	β = 92.1
c = 53.394	γ = 111.14

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS V		2012-12-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B2	1.0	SPring-8	BL26B2

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	50	92.7	0.042	44.12	3.9		26552			22.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.03	57.2		0.127	0.993		3.8

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2PBR	2	50	25215	1335	92.38	0.18875	0.18587	0.2	0.24395	0.25	RANDOM	40.726

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]
-3.04	2.36	2.1	1.92	4.39	-2.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.943
r_dihedral_angle_4_deg	18.754
r_dihedral_angle_3_deg	15.902
r_long_range_B_refined	6.945
r_long_range_B_other	6.944
r_scangle_other	5.979
r_dihedral_angle_1_deg	5.909
r_mcangle_it	4.38
r_mcangle_other	4.379
r_scbond_it	4.378
r_scbond_other	4.33
r_mcbond_other	3.39
r_mcbond_it	3.389
r_angle_refined_deg	1.854
r_angle_other_deg	1.086
r_chiral_restr	0.107
r_bond_refined_d	0.017
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.003
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3010
Nucleic Acid Atoms
Solvent Atoms	136
Heterogen Atoms	52

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing