☰ Navigation Tabs
x-ray structure of the WlaRB TDP-quinovose 3,4-ketoisomerase from campylobacter jejuni
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PA7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 100 mM HEPES, 16-18% PEG-8000, 200 mM LiCl, 5 mM TDP
Crystal Properties Matthews coefficient Solvent content 2.28 46.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.6 α = 90 b = 104.6 β = 90 c = 93.9 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD Bruker Platinum 135 montel 2016-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2 50 99.7 0.083 0.083 12.7 9.5 39376
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.1 99.1 0.36 2.8 4.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2PA7 2 30 37330 2017 99.75 0.18284 0.17946 0.1854 0.2449 0.2448 RANDOM 27.169
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 -0.04 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.083 r_dihedral_angle_4_deg 25.107 r_dihedral_angle_3_deg 18.223 r_dihedral_angle_1_deg 7.271 r_long_range_B_refined 6.947 r_long_range_B_other 6.901 r_scangle_other 5.342 r_scbond_other 3.501 r_scbond_it 3.497 r_mcangle_it 3.494
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.083 r_dihedral_angle_4_deg 25.107 r_dihedral_angle_3_deg 18.223 r_dihedral_angle_1_deg 7.271 r_long_range_B_refined 6.947 r_long_range_B_other 6.901 r_scangle_other 5.342 r_scbond_other 3.501 r_scbond_it 3.497 r_mcangle_it 3.494 r_mcangle_other 3.494 r_mcbond_it 2.485 r_mcbond_other 2.474 r_angle_refined_deg 2.004 r_angle_other_deg 0.951 r_chiral_restr 0.122 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 4300 Nucleic Acid Atoms Solvent Atoms 287 Heterogen Atoms 102
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling PHASER phasing