1H48

The structure of 2C-Methyl-D-erythritol 2,4-cyclodiphosphate synthase in complex with CMP and product


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.610-20% PEG 2000 MONOETHYL ETHER, 0.1M AMMONIUM SULPHATE, 0.1M SODIUM ACETATE, pH 5.60
Crystal Properties
Matthews coefficientSolvent content
3.665.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 198.122α = 90
b = 150.287β = 106.52
c = 57.559γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1002002-05-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.32098.60.05418.23.1731322
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)
12.32.3886.30.611.63.1

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1GX12.32067711359799.90.2040.2020.236RANDOM50.89
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]
1.511.07-0.81-0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.466
r_scangle_it3.412
r_scbond_it2.037
r_mcangle_it1.531
r_angle_refined_deg1.333
r_mcbond_it0.815
r_nbd_refined0.301
r_xyhbond_nbd_refined0.167
r_symmetry_vdw_refined0.154
r_symmetry_hbond_refined0.146
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.466
r_scangle_it3.412
r_scbond_it2.037
r_mcangle_it1.531
r_angle_refined_deg1.333
r_mcbond_it0.815
r_nbd_refined0.301
r_xyhbond_nbd_refined0.167
r_symmetry_vdw_refined0.154
r_symmetry_hbond_refined0.146
r_chiral_restr0.082
r_metal_ion_refined0.081
r_bond_refined_d0.012
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7084
Nucleic Acid Atoms
Solvent Atoms187
Heterogen Atoms268

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing