5B49

Crystal structure of LpxH with manganese from Pseudomonas aeruginosa


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.62930.2M L-Proline, 0.1M HEPES pH 7.6, 8.5% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.3948.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.937α = 90
b = 108.862β = 92.68
c = 51.555γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2011-02-17MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.0000, 1.8925SPring-8BL41XU

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
11.65501000.07520.46.764565
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)
11.651.711000.4852.236.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT1.6529.2361172330099.680.152880.151620.17662RANDOM21.893
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]
0.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.629
r_dihedral_angle_4_deg15.669
r_dihedral_angle_3_deg11.586
r_long_range_B_refined6.612
r_long_range_B_other6.357
r_scangle_other5.477
r_dihedral_angle_1_deg5.467
r_scbond_it3.605
r_scbond_other3.599
r_mcangle_it2.671
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.629
r_dihedral_angle_4_deg15.669
r_dihedral_angle_3_deg11.586
r_long_range_B_refined6.612
r_long_range_B_other6.357
r_scangle_other5.477
r_dihedral_angle_1_deg5.467
r_scbond_it3.605
r_scbond_other3.599
r_mcangle_it2.671
r_mcangle_other2.671
r_mcbond_it1.965
r_mcbond_other1.963
r_angle_refined_deg1.403
r_angle_other_deg0.971
r_chiral_restr0.052
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3942
Nucleic Acid Atoms
Solvent Atoms580
Heterogen Atoms118

Software

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