4EW2

The structure of human glycinamide ribonucleotide transformylase in complex with 10S-methylthio-DDATHF.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.22980.1 M phosphate/citrate buffer, 1.5-2.0 M ammonium sulfate at p.H 4.2. 25% Glycerol added as cryoprotectant, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
4.4672.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.173α = 90
b = 78.173β = 90
c = 229.348γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat mirror (vertical focusing), single crystal Si(111) bent monochromator (horizontal focusing)2007-11-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.9795SSRLBL11-1

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
11.667.7399.90.0457.211.85559324.8
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)
11.61.661000.5424125431

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 DIFFRACTIONTHROUGHOUT1.60267.7355466281499.860.1820.1810.211RANDOM26.919
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]
0.450.220.45-0.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.145
r_dihedral_angle_4_deg13.586
r_dihedral_angle_3_deg12.577
r_sphericity_free8.241
r_dihedral_angle_1_deg5.748
r_sphericity_bonded5.422
r_scangle_it4.939
r_scbond_it3.805
r_rigid_bond_restr3.322
r_mcangle_it2.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.145
r_dihedral_angle_4_deg13.586
r_dihedral_angle_3_deg12.577
r_sphericity_free8.241
r_dihedral_angle_1_deg5.748
r_sphericity_bonded5.422
r_scangle_it4.939
r_scbond_it3.805
r_rigid_bond_restr3.322
r_mcangle_it2.309
r_angle_refined_deg1.669
r_mcbond_it1.529
r_angle_other_deg1.237
r_mcbond_other0.981
r_chiral_restr0.099
r_bond_refined_d0.017
r_gen_planes_refined0.007
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1554
Nucleic Acid Atoms
Solvent Atoms281
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling