2PX7

Crystal structure of 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase from Thermus thermophilus HB8


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YE7PDB entry 1YE7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8293USING 2 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (6.36 mg/ml) AND RESERVOIR SOLUTION CONTAINING 0.9M Li Sulfate, 0.09M HEPES pH 8.0, 0.01M Betaine, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.3463.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.084α = 90
b = 104.084β = 90
c = 107.76γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU JUPITER 2102007-03-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B21.00000SPring-8BL26B2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.2501000.04325.61133616
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.22.281000.286113339

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 1YE72.25033570169999.940.2280.2270.248RANDOM37.878
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]
1.050.531.05-1.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.015
r_dihedral_angle_4_deg20.604
r_dihedral_angle_3_deg15.689
r_dihedral_angle_1_deg8.895
r_scangle_it3.451
r_scbond_it2.048
r_angle_refined_deg1.467
r_mcangle_it1.426
r_mcbond_it0.775
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.015
r_dihedral_angle_4_deg20.604
r_dihedral_angle_3_deg15.689
r_dihedral_angle_1_deg8.895
r_scangle_it3.451
r_scbond_it2.048
r_angle_refined_deg1.467
r_mcangle_it1.426
r_mcbond_it0.775
r_nbtor_refined0.302
r_nbd_refined0.222
r_symmetry_hbond_refined0.215
r_xyhbond_nbd_refined0.168
r_symmetry_vdw_refined0.167
r_chiral_restr0.1
r_bond_refined_d0.013
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3006
Nucleic Acid Atoms
Solvent Atoms160
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction