3LD9 | pdb_00003ld9

Crystal structure of thymidylate kinase from Ehrlichia chaffeensis at 2.15A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2PBR	PDB ENTRY 2PBR MODIFIED WITH CCP4 PROGRAM CHAINSAW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	290	MD PACT SCREEN G8: 100MM BIS-TRIS-PROPANE PH 7.5, 200MM NA-SULPHATE, 20% PEG 3350; EHCHA.01616.A AT 25.5MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.17	α = 90
b = 144.82	β = 90
c = 146.84	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	ADSC QUANTUM 315r	Single crystal, cylindrically bent, Si(220)	2009-12-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.9744	ALS	5.0.1

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	2.15	50	100	0.079	16.84	5.9	46727	46708		-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	2.15	2.21	99.9		0.481	3.7	5.8

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 2PBR MODIFIED WITH CCP4 PROGRAM CHAINSAW	2.15	46.37	46727	44279	2354	99.97	0.18883	0.18656	0.2	0.2322	0.25	RANDOM	31.523

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]
0.47			-2.03		1.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.035
r_dihedral_angle_4_deg	22.633
r_dihedral_angle_3_deg	13.267
r_dihedral_angle_1_deg	5.192
r_scangle_it	3.36
r_scbond_it	2.112
r_angle_refined_deg	1.345
r_mcangle_it	1.295
r_angle_other_deg	0.906
r_mcbond_it	0.71
r_mcbond_other	0.208
r_chiral_restr	0.076
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5700
Nucleic Acid Atoms
Solvent Atoms	301
Heterogen Atoms	28

Software

Software
Software Name	Purpose
BOS	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling