1T0A

Crystal Structure of 2C-Methyl-D-Erythritol-2,4-cyclodiphosphate Synthase from Shewanella Oneidensis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GX1PDB entry 1GX1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.8295formate, glycerol, TRIS, sodium chloride, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
3.665.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.088α = 90
b = 117.088β = 90
c = 108.937γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBRUKER SMART 6000Montel mirrors2003-07-17MSINGLE WAVELENGTH
21x-ray100CCDBRANDEIS - B4beam focused by a toroidal mirror2003-07-29MMAD
1,21
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEENRAF-NONIUS FR5911.5418
2SYNCHROTRONNSLS BEAMLINE X12C.97911NSLSX12C

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
1,21.681.650.0810.08155.714.59985422
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)
1,21.61.661000.50.55.913.1

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1GX11.629.89985494783498699.970.175260.174340.19307RANDOM15.215
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]
-0.17-0.170.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.808
r_scangle_it4.55
r_scbond_it2.87
r_mcangle_it1.774
r_angle_refined_deg1.603
r_mcbond_it1.005
r_angle_other_deg0.884
r_symmetry_hbond_refined0.334
r_nbd_other0.254
r_nbd_refined0.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.808
r_scangle_it4.55
r_scbond_it2.87
r_mcangle_it1.774
r_angle_refined_deg1.603
r_mcbond_it1.005
r_angle_other_deg0.884
r_symmetry_hbond_refined0.334
r_nbd_other0.254
r_nbd_refined0.23
r_xyhbond_nbd_refined0.208
r_symmetry_vdw_other0.205
r_metal_ion_refined0.121
r_chiral_restr0.111
r_symmetry_vdw_refined0.086
r_nbtor_other0.083
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_gen_planes_other0.003
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3555
Nucleic Acid Atoms
Solvent Atoms583
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing