3FBA

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 1GX1PDB ENTRY 1GX1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.62980.2M potassium sodium tartate tetrahydrate, tri-sodium citrate dihydrate, pH5.6, 2.0M ammonium sulphate, vapor diffusion, hanging drop, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
7.180

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 144.127α = 90
b = 144.127β = 90
c = 144.127γ = 90
Symmetry
Space GroupI 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC Q210 2Dmirrors2004-04-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.9756ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
13.129.4299.90.1010.1016.18812.291879178
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)
13.13.271000.3260.3262.312.51318

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1GX13.124.729187916043699.910.1870.1870.1860.198RANDOM55.168
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_deg34.953
r_dihedral_angle_3_deg16.277
r_dihedral_angle_4_deg15.927
r_dihedral_angle_1_deg5.391
r_scangle_it1.902
r_angle_refined_deg1.612
r_scbond_it1.136
r_mcangle_it0.974
r_mcbond_it0.547
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.953
r_dihedral_angle_3_deg16.277
r_dihedral_angle_4_deg15.927
r_dihedral_angle_1_deg5.391
r_scangle_it1.902
r_angle_refined_deg1.612
r_scbond_it1.136
r_mcangle_it0.974
r_mcbond_it0.547
r_nbtor_refined0.307
r_nbd_refined0.212
r_symmetry_vdw_refined0.211
r_xyhbond_nbd_refined0.172
r_symmetry_hbond_refined0.136
r_chiral_restr0.118
r_bond_refined_d0.013
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1183
Nucleic Acid Atoms
Solvent Atoms37
Heterogen Atoms47

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction