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Crystal structure of beta-decarboxylating dehydrogenase (TK0280) from Thermococcus kodakarensis complexed with Mn and homoisocitrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HN3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 2-propanol, HEPES, sodium chloride
Crystal Properties Matthews coefficient Solvent content 5.99 79.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.669 α = 90 b = 113.669 β = 90 c = 143.226 γ = 90
Symmetry Space Group P 43 21 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 2014-06-28 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 2.64 143.23 99.2 0.085 41.8 7.7 28294
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 2.64 2.69 100 0.594 3.9 7.8
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 5HN3 2.64 143.23 26653 1342 99.09 0.20206 0.20113 0.2058 0.22033 0.2225 RANDOM 66.852
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] 0.02 0.02 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.963 r_dihedral_angle_4_deg 20.103 r_dihedral_angle_3_deg 17.849 r_long_range_B_other 9.555 r_long_range_B_refined 9.554 r_scangle_other 7.729 r_mcangle_other 6.28 r_mcangle_it 6.276 r_dihedral_angle_1_deg 6.164 r_scbond_it 5.147
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.963 r_dihedral_angle_4_deg 20.103 r_dihedral_angle_3_deg 17.849 r_long_range_B_other 9.555 r_long_range_B_refined 9.554 r_scangle_other 7.729 r_mcangle_other 6.28 r_mcangle_it 6.276 r_dihedral_angle_1_deg 6.164 r_scbond_it 5.147 r_scbond_other 5.145 r_mcbond_it 4.432 r_mcbond_other 4.414 r_angle_refined_deg 1.555 r_angle_other_deg 0.899 r_chiral_restr 0.098 r_bond_refined_d 0.012 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 2505 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement Coot model building HKL-2000 data scaling PHASER phasing HKL-2000 data reduction