2J65

Structure of LpxC from Aquifex aeolicus in complex with UDP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5293CRYSTALS OF LPXC WERE GROWN BY HANGING VAPOR DIFFUSION AT 20 DEG C USING 1 UL OF PROTEIN (184 UM) AND 1 UL OF A RESERVOIR SOLUTION CONTAINING 8% PEG 6000, 100 MM TRIS, PH 8.5, AND 300 MM NACL.
Crystal Properties
Matthews coefficientSolvent content
2.6953.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.755α = 90
b = 101.755β = 90
c = 124.243γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHPT-COATED MIRRORS, MICROFOCUS BEAMLINE2006-05-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-2ESRFID23-2

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
12.250.9990.1111.33.936577
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)
12.22.3298.50.483.63.9

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 1P422.250.934736183698.90.1710.1680.225RANDOM22.83
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]
-0.86-0.43-0.861.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.024
r_dihedral_angle_4_deg21.107
r_dihedral_angle_3_deg14.182
r_dihedral_angle_1_deg5.973
r_scangle_it2.701
r_scbond_it1.671
r_angle_refined_deg1.34
r_mcangle_it1.058
r_mcbond_it0.653
r_nbtor_refined0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.024
r_dihedral_angle_4_deg21.107
r_dihedral_angle_3_deg14.182
r_dihedral_angle_1_deg5.973
r_scangle_it2.701
r_scbond_it1.671
r_angle_refined_deg1.34
r_mcangle_it1.058
r_mcbond_it0.653
r_nbtor_refined0.3
r_symmetry_hbond_refined0.199
r_nbd_refined0.187
r_symmetry_vdw_refined0.178
r_xyhbond_nbd_refined0.142
r_chiral_restr0.105
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_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 Atoms4314
Nucleic Acid Atoms
Solvent Atoms488
Heterogen Atoms107

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing