4EW3

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MEOPDB ENTRY 1MEO

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 , VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
4.4772.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.124α = 90
b = 78.124β = 90
c = 230.048γ = 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
11.767.7399.90.04238.37.84658828.9
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)
11.71.7699.70.69638.3104512

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1MEO1.70267.7346452234999.80.20.20.215RANDOM29.368
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]
-0.37-0.18-0.370.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.691
r_dihedral_angle_4_deg18.714
r_dihedral_angle_3_deg13.108
r_sphericity_free10.533
r_sphericity_bonded7.212
r_dihedral_angle_1_deg5.668
r_scangle_it4.784
r_scbond_it3.229
r_mcangle_it2.385
r_rigid_bond_restr1.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.691
r_dihedral_angle_4_deg18.714
r_dihedral_angle_3_deg13.108
r_sphericity_free10.533
r_sphericity_bonded7.212
r_dihedral_angle_1_deg5.668
r_scangle_it4.784
r_scbond_it3.229
r_mcangle_it2.385
r_rigid_bond_restr1.71
r_angle_refined_deg1.676
r_mcbond_it1.568
r_angle_other_deg1.131
r_mcbond_other1.074
r_chiral_restr0.1
r_bond_refined_d0.018
r_gen_planes_refined0.008
r_gen_planes_other0.003
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1554
Nucleic Acid Atoms
Solvent Atoms167
Heterogen Atoms48

Software

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