2IXI

RmlC P aeruginosa with dTDP-xylose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2IXJPDB ENTRY 2IXJ

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.2344.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.785α = 90
b = 148.065β = 90
c = 45.434γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX9.6SRSPX9.6

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
11.844800.15.2335190
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)
11.81.9670.3523

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 2IXJ1.874.5431529166480.20.1880.1860.237RANDOM18.41
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]
3.51-2.51-1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.923
r_dihedral_angle_4_deg17.944
r_dihedral_angle_3_deg13.455
r_dihedral_angle_1_deg6.637
r_scangle_it1.85
r_angle_refined_deg1.609
r_scbond_it1.243
r_angle_other_deg0.759
r_mcangle_it0.71
r_mcbond_it0.657
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.923
r_dihedral_angle_4_deg17.944
r_dihedral_angle_3_deg13.455
r_dihedral_angle_1_deg6.637
r_scangle_it1.85
r_angle_refined_deg1.609
r_scbond_it1.243
r_angle_other_deg0.759
r_mcangle_it0.71
r_mcbond_it0.657
r_symmetry_vdw_other0.278
r_nbd_refined0.196
r_symmetry_vdw_refined0.195
r_nbd_other0.182
r_nbtor_refined0.177
r_symmetry_hbond_refined0.165
r_xyhbond_nbd_refined0.133
r_chiral_restr0.084
r_nbtor_other0.077
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.002
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 Atoms2982
Nucleic Acid Atoms
Solvent Atoms455
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling