4DWJ | pdb_00004dwj

Crystal structure of Thymidylate Kinase from Staphylococcus aureus in complex with Thymidine Monophosphate

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	0.2 M MgCl2, 0.1 M HEPES, 25 % PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.662	α = 81.48
b = 73.409	β = 90.1
c = 96.868	γ = 90.12

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	CCD	MARMOSAIC 300 mm CCD	MIRROR	2011-11-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.97886	APS	21-ID-D

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	2.74	30	95.2	0.07	13.27	1.9	39979	39979		-3	71.7

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)
1	2.75	2.8	98.3		0.41	1.9	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	pdb entry 2CCJ	2.74	30	37963	37963	2016	94.71	0.20412	0.20065	0.2053	0.26817	0.2665	RANDOM	57.257

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]
5.15	-0.26	-0.55	-4.26	3.12	-1.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.661
r_dihedral_angle_4_deg	13.092
r_dihedral_angle_3_deg	10.399
r_dihedral_angle_1_deg	2.341
r_angle_refined_deg	1.744
r_angle_other_deg	1.108
r_chiral_restr	0.101
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_gen_planes_other	0.004
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12722
Nucleic Acid Atoms
Solvent Atoms	75
Heterogen Atoms	120

Software

Software
Software Name	Purpose
Blu-Ice	data collection
MOLREP	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling