1ZLY

The structure of human glycinamide ribonucleotide transformylase in complex with alpha,beta-N-(hydroxyacetyl)-D-ribofuranosylamine and 10-formyl-5,8,dideazafolate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP63005 mg/ml protein in 10 mM Hepes pH 7.5, 1 mM DTE 1:1 with well solution (100 mM Na citrate pH 6.0, 20% 2-propanol (v/v), 20% PEG-4000 (w/v)) , VAPOR DIFFUSION, HANGING DROP, temperature 300K
2VAPOR DIFFUSION, SITTING DROP6.33005 mg/ml protein in 10 mM Hepes pH 7.5, 1 mM DTE 1:1 with well solution (100 mM Na citrate pH 6.0, 6-8% 2-propanol (v/v), 16-18% PEG-4000 (w/v)) , pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 300K

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.9α = 90
b = 75.9β = 90
c = 101γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray282IMAGE PLATERIGAKU RAXIS IIC1997-02-25MSINGLE WAVELENGTH
21x-ray110CCDADSC QUANTUM 41997-08-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418
2SYNCHROTRONCHESS BEAMLINE F20.68CHESSF2

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
1,22.074099.50.0737.73.921205199152153.8
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)
2.072.1730.2963.7

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT1ZLX2.0740219915189001015950.2220.20.190.236Selected53.8
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]
-5.79-3.49-5.7911.59
RMS Deviations
KeyRefinement Restraint Deviation
c_mcbond_it2.94
c_angle_deg1.45
c_bond_d0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1507
Nucleic Acid Atoms
Solvent Atoms253
Heterogen Atoms43

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement