Experiment: 2PBR

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2CCJ	PDN ENTRY 2CCJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.6	293	0.1 M ADA, 0.05 M Lithium Sulfate, 12% PEG 4000, 2% iso-propanol, 3% D(+)-sucrose as additive, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.765	α = 95.19
b = 50.478	β = 90.81
c = 52.823	γ = 111.68

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	RH Coated Bent-Cyrindrical MIRROR	2006-06-30	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)	R Sym 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	1.95	50	93.9	0.042	0.051			75100	27384			18.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2.02	76.8		0.177	0.191			2254

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	PDN ENTRY 2CCJ	1.96	32.48	26353	2527	89.8	0.194	0.194	0.1968	0.242	0.244	RANDOM	29.2

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]
-6.14	2.43	6.92	2.88	11.8	3.26

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	20.7
c_angle_deg	1.3
c_bond_d	0.005
c_improper_angle_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3156
Nucleic Acid Atoms
Solvent Atoms	320
Heterogen Atoms	10

Software

Software
Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing