1G3L

THE STRUCTURAL BASIS OF THE CATALYTIC MECHANISM AND REGULATION OF GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE (RMLA). TDP-L-RHAMNOSE COMPLEX.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1G1L 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP429210 % (w/v) PEG 6000, 0.2 M Li-sulfate, 0.1 M Na-citrate pH 4.0; protein incubated with 10 mM dTDP-L-rhamnose, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.5545.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.087α = 90
b = 138.557β = 90
c = 139.676γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS2000-03-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.749.994.20.126.87.23631137.11
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.82.8470.80.2662.95.7

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 DIFFRACTIONTHROUGHOUT1G1L2.710034462181593.80.2050.2040.23RANDOM12.78
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]
1.070.01-1.08
RMS Deviations
KeyRefinement Restraint Deviation
p_scangle_it1.772
p_scbond_it1.097
p_mcangle_it0.847
p_mcbond_it0.48
p_chiral_restr0.102
p_bond_d0.014
p_plane_restr0.006
p_angle_d
p_angle_deg
p_planar_d
RMS Deviations
KeyRefinement Restraint Deviation
p_scangle_it1.772
p_scbond_it1.097
p_mcangle_it0.847
p_mcbond_it0.48
p_chiral_restr0.102
p_bond_d0.014
p_plane_restr0.006
p_angle_d
p_angle_deg
p_planar_d
p_hb_or_metal_coord
p_singtor_nbd
p_multtor_nbd
p_xhyhbond_nbd
p_xyhbond_nbd
p_planar_tor
p_staggered_tor
p_orthonormal_tor
p_transverse_tor
p_special_tor
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9148
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms305

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling