2UZH

Mycobacterium smegmatis 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase (IspF)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.518% PEG 8000, 0.1 M SODIUM CACODYLATE PH 6.5, 0.2 M CALCIUM ACETATE
Crystal Properties
Matthews coefficientSolvent content
3.1560.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 159.121α = 90
b = 159.121β = 90
c = 54.16γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHPT COATED MIRRORS IN A KIRKPATRICK-BAEZ (KB) GEOMETRY2006-05-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-2ESRFID23-2

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
12.251.395.40.0863.533193
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)
12.23.1176.30.351.72.1

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 1GX12.251.33170216711000.1650.1630.206RANDOM28.25
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]
-0.14-0.140.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.135
r_dihedral_angle_4_deg22.03
r_dihedral_angle_3_deg17.5
r_dihedral_angle_1_deg6.267
r_scangle_it3.923
r_mcangle_it3.633
r_scbond_it2.669
r_mcbond_it2.488
r_angle_refined_deg1.57
r_nbtor_refined0.293
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.135
r_dihedral_angle_4_deg22.03
r_dihedral_angle_3_deg17.5
r_dihedral_angle_1_deg6.267
r_scangle_it3.923
r_mcangle_it3.633
r_scbond_it2.669
r_mcbond_it2.488
r_angle_refined_deg1.57
r_nbtor_refined0.293
r_nbd_refined0.214
r_symmetry_hbond_refined0.211
r_symmetry_vdw_refined0.181
r_xyhbond_nbd_refined0.178
r_chiral_restr0.101
r_bond_refined_d0.013
r_gen_planes_refined0.005
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_refined
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 Atoms3275
Nucleic Acid Atoms
Solvent Atoms272
Heterogen Atoms136

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing