2VES

Crystal Structure of LpxC from Pseudomonas aeruginosa complexed with the potent BB-78485 inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1P42PDB ENTRY 1P42

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5PALPXC, 10 MG/ML IN 25 MM HEPES PH 7.0, 2 MM TCEP, 0.3 M NACL, 1MM ZNCL2. BB-78485 ADDED TO 1 MM. HANGING DROP, 0.1 M SODIUM CACODYLATE PH 6.5, 0.2 M AMMONIUM SULFATE AND 10 % PEG 8000, 10 MM ZNCL2.
Crystal Properties
Matthews coefficientSolvent content
2.1350.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.542α = 90
b = 103.331β = 90
c = 105.284γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray173CCDADSC CCDMIRRORS2004-12-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-IDAPS17-ID

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
11.934.1599.90.0823.616.478112
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)
11.91.9799.50.522.55.7

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 1P421.973.7274089392799.60.1790.1770.221RANDOM23.05
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]
0.75-0.830.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.124
r_dihedral_angle_4_deg15.259
r_dihedral_angle_3_deg12.611
r_dihedral_angle_1_deg5.822
r_scangle_it1.856
r_scbond_it1.289
r_angle_refined_deg1.122
r_angle_other_deg1.024
r_mcangle_it0.768
r_mcbond_it0.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.124
r_dihedral_angle_4_deg15.259
r_dihedral_angle_3_deg12.611
r_dihedral_angle_1_deg5.822
r_scangle_it1.856
r_scbond_it1.289
r_angle_refined_deg1.122
r_angle_other_deg1.024
r_mcangle_it0.768
r_mcbond_it0.67
r_symmetry_vdw_other0.262
r_nbd_refined0.196
r_nbtor_refined0.172
r_nbd_other0.168
r_symmetry_vdw_refined0.162
r_symmetry_hbond_refined0.155
r_xyhbond_nbd_refined0.126
r_chiral_restr0.101
r_nbtor_other0.079
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_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 Atoms6863
Nucleic Acid Atoms
Solvent Atoms1223
Heterogen Atoms107

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing