3SH0

Crystal Structure of E. coli undecaprenyl pyrophosphate synthase in complex with BPH-1065


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2E98pdb entry 2E98

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529850mM HEPES, pH 7.5, 5% PEG 4,000, vapor diffusion, hanging drop, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1242.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.765α = 90
b = 68.724β = 90
c = 112.056γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298CCDMARMOSAIC 300 mm CCD2010-06-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D0.9787APS21-ID-D

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
11.845099.30.0658.1104256011
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)
11.841.8789.20.6425.31870

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 2E981.8435.714448342354212998.960.17040.17040.16830.2111RANDOM30.229
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]
0.01-0.070.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.569
r_dihedral_angle_4_deg19.616
r_dihedral_angle_3_deg14.541
r_dihedral_angle_1_deg5.649
r_scangle_it5.185
r_scbond_it3.318
r_mcangle_it2.049
r_angle_refined_deg1.901
r_mcbond_it1.231
r_chiral_restr0.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.569
r_dihedral_angle_4_deg19.616
r_dihedral_angle_3_deg14.541
r_dihedral_angle_1_deg5.649
r_scangle_it5.185
r_scbond_it3.318
r_mcangle_it2.049
r_angle_refined_deg1.901
r_mcbond_it1.231
r_chiral_restr0.16
r_bond_refined_d0.024
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3397
Nucleic Acid Atoms
Solvent Atoms315
Heterogen Atoms69

Software

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