3G4C

Flavine dependant thymidylate syntahse S88C mutant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1O26Native structure with dUMP (PDB code: 1O26)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829540% PEG 200, 0.1M Tris-HCL, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.0138.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.897α = 90
b = 116.495β = 90
c = 140.986γ = 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, double crystal monochromator, 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
12.0546.2299.90.074124.25660056600
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.052.11000.9990.632.14.34137

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 fourierTHROUGHOUTNative structure with dUMP (PDB code: 1O26)2.0546.2253694284399.910.202480.199830.25358RANDOM25.267
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]
3.77-1.38-2.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.375
r_dihedral_angle_4_deg16.867
r_dihedral_angle_3_deg14.801
r_dihedral_angle_1_deg6.228
r_scangle_it2.519
r_scbond_it1.689
r_angle_refined_deg1.609
r_mcangle_it1.171
r_angle_other_deg0.965
r_mcbond_it0.745
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.375
r_dihedral_angle_4_deg16.867
r_dihedral_angle_3_deg14.801
r_dihedral_angle_1_deg6.228
r_scangle_it2.519
r_scbond_it1.689
r_angle_refined_deg1.609
r_mcangle_it1.171
r_angle_other_deg0.965
r_mcbond_it0.745
r_symmetry_vdw_other0.253
r_nbd_other0.208
r_nbd_refined0.202
r_mcbond_other0.202
r_symmetry_vdw_refined0.199
r_nbtor_refined0.191
r_xyhbond_nbd_refined0.157
r_symmetry_hbond_refined0.1
r_nbtor_other0.091
r_chiral_restr0.09
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d0.005
r_gen_planes_other0.002
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 Atoms6950
Nucleic Acid Atoms
Solvent Atoms167
Heterogen Atoms292

Software

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