3SGX

Crystal Structure of E. coli undecaprenyl pyrophosphate synthase in complex with BPH-1100


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
2.0339.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.95α = 90
b = 68.135β = 90
c = 111.608γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298CCDMARMOSAIC 225 mm CCD2010-08-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.9787APS21-ID-F

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
12.455096.90.092105.71722511
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)
12.452.4990.70.4514.7786

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 2E982.4532.65180051714086596.650.24580.24580.24170.3275RANDOM45.5567
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_deg36.42
r_dihedral_angle_3_deg19.578
r_dihedral_angle_4_deg18.674
r_dihedral_angle_1_deg7.45
r_scangle_it3.764
r_scbond_it2.285
r_angle_refined_deg1.682
r_mcangle_it1.487
r_mcbond_it0.791
r_chiral_restr0.107
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.42
r_dihedral_angle_3_deg19.578
r_dihedral_angle_4_deg18.674
r_dihedral_angle_1_deg7.45
r_scangle_it3.764
r_scbond_it2.285
r_angle_refined_deg1.682
r_mcangle_it1.487
r_mcbond_it0.791
r_chiral_restr0.107
r_bond_refined_d0.015
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3256
Nucleic Acid Atoms
Solvent Atoms75
Heterogen Atoms68

Software

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