3G4A

Crystal structure of flavine dependant thymidylate synthase S88A mutant from Thermotoga maritima at 1.95 angstrom resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829542% PEG 200, 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.0138.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.952α = 90
b = 116.222β = 90
c = 140.728γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat collimating mirror, toroid focusing mirror2007-03-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.9795SSRLBL9-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.9589.499.60.06613.24.46513665136
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.95299.60.6921.53.74580

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONDIFFERENCE FOURIERTHROUGHOUT1.9589.461778328899.50.187460.185650.22173RANDOM30.475
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]
3.1-0.71-2.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.649
r_dihedral_angle_4_deg17.572
r_dihedral_angle_3_deg14.439
r_dihedral_angle_1_deg6
r_scangle_it2.637
r_scbond_it1.767
r_angle_refined_deg1.588
r_mcangle_it1.211
r_angle_other_deg0.958
r_mcbond_it0.795
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.649
r_dihedral_angle_4_deg17.572
r_dihedral_angle_3_deg14.439
r_dihedral_angle_1_deg6
r_scangle_it2.637
r_scbond_it1.767
r_angle_refined_deg1.588
r_mcangle_it1.211
r_angle_other_deg0.958
r_mcbond_it0.795
r_symmetry_vdw_other0.239
r_mcbond_other0.222
r_nbd_refined0.21
r_nbd_other0.208
r_symmetry_hbond_refined0.204
r_symmetry_vdw_refined0.198
r_nbtor_refined0.192
r_xyhbond_nbd_refined0.158
r_chiral_restr0.09
r_nbtor_other0.09
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
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 AtomsNumber
Protein Atoms7042
Nucleic Acid Atoms
Solvent Atoms159
Heterogen Atoms292

Software

Software
Software NamePurpose
Blu-Icedata collection
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing