4MQB

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


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP62930.2 M MgCl2, 0.1 M MMES buffer, 20% PEG6000, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1241.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.134α = 90
b = 90.457β = 101.64
c = 49.524γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDMIRROR2013-07-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.553099.90.0620.13.75772957729-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.551.581000.522.93.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 4F4I1.5525.625477354773292999.710.145280.142410.19845RANDOM25.34
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]
-0.040.89-1.351.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.72
r_sphericity_bonded21.358
r_dihedral_angle_4_deg18.979
r_dihedral_angle_3_deg10.82
r_scangle_other9.361
r_scbond_it8.774
r_scbond_other8.536
r_long_range_B_refined7.568
r_long_range_B_other7.567
r_rigid_bond_restr7.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.72
r_sphericity_bonded21.358
r_dihedral_angle_4_deg18.979
r_dihedral_angle_3_deg10.82
r_scangle_other9.361
r_scbond_it8.774
r_scbond_other8.536
r_long_range_B_refined7.568
r_long_range_B_other7.567
r_rigid_bond_restr7.22
r_mcangle_other3.927
r_mcangle_it3.901
r_dihedral_angle_1_deg3.415
r_mcbond_it3.324
r_mcbond_other3.294
r_angle_refined_deg1.926
r_angle_other_deg0.98
r_chiral_restr0.134
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_metal_ion_other
r_metal_ion_refined
r_xyhbond_nbd_other
r_symmetry_vdw_other
r_nbtor_other
r_nbtor_refined
r_scangle_it
r_nbd_other
r_nbd_refined
r_symmetry_vdw_refined
r_symmetry_hbond_refined
r_sphericity_free
r_xyhbond_nbd_refined
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3260
Nucleic Acid Atoms
Solvent Atoms329
Heterogen Atoms26

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling