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Crystal structure of beta-decarboxylating dehydrogenase (TK0280) from Thermococcus kodakarensis complexed with Mn and isocitrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HN4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 Tris, sodium chloride, 2-methyl-2,4-pentanediol
Crystal Properties Matthews coefficient Solvent content 2.95 58.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.372 α = 90 b = 80.372 β = 90 c = 141.063 γ = 90
Symmetry Space Group P 43 2 2
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 ADSC QUANTUM 270 2014-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0 Photon Factory AR-NE3A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.55 141.06 99.2 0.08 41.2 7.7 15751
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 2.55 2.59 100 0.544 3.3 7.7
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 5HN4 2.55 141.06 14808 778 99.12 0.20032 0.19748 0.2031 0.25682 0.2576 RANDOM 66.118
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] -0.01 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.327 r_dihedral_angle_4_deg 19.152 r_dihedral_angle_3_deg 17.843 r_long_range_B_refined 8.839 r_long_range_B_other 8.837 r_scangle_other 6.934 r_dihedral_angle_1_deg 6.666 r_mcangle_it 5.664 r_mcangle_other 5.663 r_scbond_it 4.592
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.327 r_dihedral_angle_4_deg 19.152 r_dihedral_angle_3_deg 17.843 r_long_range_B_refined 8.839 r_long_range_B_other 8.837 r_scangle_other 6.934 r_dihedral_angle_1_deg 6.666 r_mcangle_it 5.664 r_mcangle_other 5.663 r_scbond_it 4.592 r_scbond_other 4.59 r_mcbond_other 3.918 r_mcbond_it 3.917 r_angle_refined_deg 1.44 r_angle_other_deg 0.887 r_chiral_restr 0.088 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 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 2495 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement Coot model building HKL-2000 data scaling PHASER phasing HKL-2000 data reduction