2GZL

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, 8% PEG 200 MME, 0.1M SODIUM ACETATE, pH 5.00, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
6.781.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 145.098α = 90
b = 145.098β = 90
c = 145.098γ = 90
Symmetry
Space GroupI 21 3

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 ID290.9330ESRFID29

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
12.528.599.8177153
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.641000.6850.6852.98.6

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 REPLACEMENTTHROUGHOUT1GX12.5301681390299.990.208550.207140.2352RANDOM51.34
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.065
r_dihedral_angle_3_deg16.557
r_dihedral_angle_4_deg14.748
r_dihedral_angle_1_deg8.683
r_scangle_it2.984
r_scbond_it1.614
r_mcangle_it1.482
r_angle_refined_deg1.256
r_mcbond_it0.923
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.065
r_dihedral_angle_3_deg16.557
r_dihedral_angle_4_deg14.748
r_dihedral_angle_1_deg8.683
r_scangle_it2.984
r_scbond_it1.614
r_mcangle_it1.482
r_angle_refined_deg1.256
r_mcbond_it0.923
r_nbtor_refined0.309
r_symmetry_vdw_refined0.216
r_nbd_refined0.207
r_symmetry_hbond_refined0.138
r_xyhbond_nbd_refined0.135
r_chiral_restr0.093
r_metal_ion_refined0.067
r_bond_refined_d0.009
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1188
Nucleic Acid Atoms
Solvent Atoms43
Heterogen Atoms64

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
CCP4data scaling