3ELC

Crystal structure of 2C-methyl-D-erythritol 2,4-clycodiphosphate synthase complexed with ligand


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GX1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.629810% glycerol, magnesium sulphate, 20% PEG 4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3748.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.676α = 90
b = 54.833β = 99.66
c = 88.506γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++mirrors2003-03-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.55047.61598922.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.52.5791.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 REPLACEMENTTHROUGHOUT1GX12.5502.2159891512781491.780.2890.2130.2080.291RANDOM48.536
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]
7.45-0.88-3-4.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.257
r_dihedral_angle_3_deg18.536
r_dihedral_angle_4_deg18.384
r_dihedral_angle_1_deg5.776
r_scangle_it2.182
r_angle_refined_deg1.378
r_scbond_it1.347
r_mcangle_it1.086
r_mcbond_it0.687
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.257
r_dihedral_angle_3_deg18.536
r_dihedral_angle_4_deg18.384
r_dihedral_angle_1_deg5.776
r_scangle_it2.182
r_angle_refined_deg1.378
r_scbond_it1.347
r_mcangle_it1.086
r_mcbond_it0.687
r_nbtor_refined0.303
r_nbd_refined0.221
r_symmetry_vdw_refined0.215
r_xyhbond_nbd_refined0.156
r_symmetry_hbond_refined0.093
r_chiral_restr0.085
r_bond_refined_d0.012
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3546
Nucleic Acid Atoms
Solvent Atoms113
Heterogen Atoms76

Software

Software
Software NamePurpose
MOSFLMdata reduction
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection