2AMT

Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase complexed with a CDP derived fluorescent inhibitor


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP52900.1M ammonium sulfate, 10% PEG 200 MME, 0.1M sodium acetate, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.6853.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.033α = 90
b = 115.269β = 90.18
c = 87.609γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210mirror2004-11-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.9756ESRFID29

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
12.329.599.40.09710.13.547682474203.929.85
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)
2.32.4299.70.2723.93.66904

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUT1GX12.329.54768245024239799.50.25820.245160.243270.27952RANDOM32.618
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]
-3.190.246.86-3.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.718
r_dihedral_angle_3_deg14.84
r_dihedral_angle_4_deg14.666
r_dihedral_angle_1_deg4.979
r_angle_refined_deg0.998
r_scangle_it0.968
r_mcangle_it0.594
r_scbond_it0.518
r_mcbond_it0.336
r_nbtor_refined0.294
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.718
r_dihedral_angle_3_deg14.84
r_dihedral_angle_4_deg14.666
r_dihedral_angle_1_deg4.979
r_angle_refined_deg0.998
r_scangle_it0.968
r_mcangle_it0.594
r_scbond_it0.518
r_mcbond_it0.336
r_nbtor_refined0.294
r_symmetry_vdw_refined0.182
r_nbd_refined0.173
r_symmetry_hbond_refined0.153
r_xyhbond_nbd_refined0.112
r_chiral_restr0.06
r_metal_ion_refined0.054
r_bond_refined_d0.006
r_gen_planes_refined0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6996
Nucleic Acid Atoms
Solvent Atoms233
Heterogen Atoms266

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing