4MQB | pdb_00004mqb

Crystal structure of thymidylate kinase from Staphylococcus aureus in complex with 2-(N-morpholino)ethanesulfonic acid

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4F4I	PDB ENTRY 4F4I

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293	0.2 M MgCl2, 0.1 M MMES buffer, 20% PEG6000, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.134	α = 90
b = 90.457	β = 101.64
c = 49.524	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	100	CCD	MARMOSAIC 300 mm CCD	MIRROR	2013-07-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

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	1.55	30	99.9	0.06	20.1	3.7	57729	57729		-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	1.55	1.58	100		0.52	2.9	3.3

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 4F4I	1.55	25.62	54773	54773	2929	99.71	0.14528	0.14241	0.16	0.19845	0.21	RANDOM	25.34

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]
-0.04		0.89	-1.35		1.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.72
r_sphericity_bonded	21.358
r_dihedral_angle_4_deg	18.979
r_dihedral_angle_3_deg	10.82
r_scangle_other	9.361
r_scbond_it	8.774
r_scbond_other	8.536
r_long_range_B_refined	7.568
r_long_range_B_other	7.567
r_rigid_bond_restr	7.22
r_mcangle_other	3.927
r_mcangle_it	3.901
r_dihedral_angle_1_deg	3.415
r_mcbond_it	3.324
r_mcbond_other	3.294
r_angle_refined_deg	1.926
r_angle_other_deg	0.98
r_chiral_restr	0.134
r_bond_refined_d	0.017
r_gen_planes_refined	0.008
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_scangle_it
r_sphericity_free

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3260
Nucleic Acid Atoms
Solvent Atoms	329
Heterogen Atoms	26

Software

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