2CCK | pdb_00002cck

CRYSTAL STRUCTURE OF UNLIGANDED S. AUREUS THYMIDYLATE KINASE

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.2		1M LICL, 0.1M NA CACODYLATE, PH7.2, 16% PEG 6000, pH 7.20

Crystal Properties
Matthews coefficient	Solvent content
2.21	43.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.26	α = 90
b = 89.88	β = 99.92
c = 50.15	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	105	IMAGE PLATE	MARRESEARCH	MIRRORS	2005-01-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007

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	2.2	30	95.6	0.04	50.1	3.4		19676			27.3

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	2.2	2.28	78		0.09	18	2.8

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	PDB ENTRY 2CCG	2.21	22.71	19669	955	96.4	0.197	0.197	0.2	0.255	0.25	RANDOM	46.5

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]
9.04		17.79	-12.46		3.42

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	19.9
c_scangle_it	11.22
c_scbond_it	8.46
c_mcangle_it	6.14
c_mcbond_it	4.7
c_angle_deg	1.2
c_improper_angle_d	0.8
c_bond_d	0.006
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3084
Nucleic Acid Atoms
Solvent Atoms	216
Heterogen Atoms	9

Software

Software
Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing