3TH8

Structure of E. coli undecaprenyl diphosphate synthase complexed with BPH-1063


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2E98PDB ENTRY 2E98

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5298.155% PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.15K
Crystal Properties
Matthews coefficientSolvent content
1.8533.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.603α = 90
b = 68.862β = 90
c = 112.297γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray123CCDMARMOSAIC 225 mm CCD2010-04-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.1145098.22797111
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.1142.16100

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 2E982.11441.82904627646140097.10.25250.25250.24950.3086RANDOM35.9978
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]
-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.797
r_dihedral_angle_4_deg19.481
r_dihedral_angle_3_deg15.314
r_dihedral_angle_1_deg7.122
r_scangle_it5.15
r_scbond_it3.236
r_mcangle_it2.104
r_angle_refined_deg1.791
r_mcbond_it1.186
r_chiral_restr0.125
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.797
r_dihedral_angle_4_deg19.481
r_dihedral_angle_3_deg15.314
r_dihedral_angle_1_deg7.122
r_scangle_it5.15
r_scbond_it3.236
r_mcangle_it2.104
r_angle_refined_deg1.791
r_mcbond_it1.186
r_chiral_restr0.125
r_bond_refined_d0.021
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3312
Nucleic Acid Atoms
Solvent Atoms63
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing