2X4G

Crystal structure of PA4631, a nucleoside-diphosphate-sugar epimerase from Pseudomonas aeruginosa


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
182.55M NACL, 0.1M HEPES PH 8 OR 2.9M NACL, 0.1M BICINE PH 8.5 AT A PROTEIN CONCENTRATION OF 2 MG ML-1.CRYSTALS WERE CRYOPROTECTED DIRECTLY IN THIS SOLUTION SUPPLEMENTED WITH 18% GLYCEROL. CRYSTAL WAS SOAKED IN 20MM TRIMETHYLLEADCHLORIDE FOR APPROXIMATELY 5 MINUTES BEFORE BEING BACK SOAKED IN CRYO BUFFER
Crystal Properties
Matthews coefficientSolvent content
2.9157.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.38α = 90
b = 83.38β = 90
c = 215.72γ = 120
Symmetry
Space GroupP 62 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRRORS2008-07-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
12.6541.7970.0823.3512600
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)
12.652.7900.662.753.4

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 DIFFRACTIONSADTHROUGHOUTNONE2.6541.712600679970.213460.211420.25314RANDOM30.888
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]
0.920.460.92-1.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.401
r_dihedral_angle_4_deg18.631
r_dihedral_angle_3_deg16.635
r_dihedral_angle_1_deg6.319
r_scangle_it2.945
r_scbond_it1.691
r_angle_refined_deg1.332
r_mcangle_it1.111
r_angle_other_deg0.845
r_mcbond_it0.564
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.401
r_dihedral_angle_4_deg18.631
r_dihedral_angle_3_deg16.635
r_dihedral_angle_1_deg6.319
r_scangle_it2.945
r_scbond_it1.691
r_angle_refined_deg1.332
r_mcangle_it1.111
r_angle_other_deg0.845
r_mcbond_it0.564
r_mcbond_other0.078
r_chiral_restr0.07
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
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_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 Atoms2301
Nucleic Acid Atoms
Solvent Atoms42
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALEPACKdata scaling
SHELXCDEphasing