5TPU

x-ray structure of the WlaRB TDP-quinovose 3,4-ketoisomerase from campylobacter jejuni


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5293100 mM HEPES, 16-18% PEG-8000, 200 mM LiCl, 5 mM TDP
Crystal Properties
Matthews coefficientSolvent content
2.2846.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.6α = 90
b = 104.6β = 90
c = 93.9γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 135montel2016-07-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
125099.70.0830.08312.79.539376
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)
122.199.10.362.84.2

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 REPLACEMENTTHROUGHOUT2PA723037330201799.750.182840.179460.2449RANDOM27.169
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]
-0.04-0.02-0.040.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.083
r_dihedral_angle_4_deg25.107
r_dihedral_angle_3_deg18.223
r_dihedral_angle_1_deg7.271
r_long_range_B_refined6.947
r_long_range_B_other6.901
r_scangle_other5.342
r_scbond_other3.501
r_scbond_it3.497
r_mcangle_it3.494
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.083
r_dihedral_angle_4_deg25.107
r_dihedral_angle_3_deg18.223
r_dihedral_angle_1_deg7.271
r_long_range_B_refined6.947
r_long_range_B_other6.901
r_scangle_other5.342
r_scbond_other3.501
r_scbond_it3.497
r_mcangle_it3.494
r_mcangle_other3.494
r_mcbond_it2.485
r_mcbond_other2.474
r_angle_refined_deg2.004
r_angle_other_deg0.951
r_chiral_restr0.122
r_bond_refined_d0.013
r_gen_planes_refined0.008
r_bond_other_d0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4300
Nucleic Acid Atoms
Solvent Atoms287
Heterogen Atoms102

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing