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Crystal structure of BioU (K124A) from Synechocystis sp.PCC6803 in complex with NAD+ and the analog of reaction intermediate, 3-(1-aminoethyl)-nonanedioic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ITD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 28% PEG 3350, 0.2M Ammonium formate, 0.1M HEPES-NaOH (pH7.0), 5mM 3-(1-aminoethyl)-nonanedioic acid, 5mM NAD+
Crystal Properties Matthews coefficient Solvent content 1.87 34.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.414 α = 90 b = 70.414 β = 90 c = 98.778 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 270 2018-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 2.5 50 100 0.1 0.034 0.993 28.5 9.6 10264
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.54 0.646 0.212 0.901
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 6ITD 2.5 38.41 9754 486 99.94 0.17797 0.17368 0.178 0.26874 0.267 RANDOM 54.314
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] 1.04 0.52 1.04 -3.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.496 r_dihedral_angle_3_deg 19.746 r_dihedral_angle_4_deg 11.755 r_long_range_B_other 8.378 r_long_range_B_refined 8.377 r_dihedral_angle_1_deg 7.397 r_scangle_other 6.383 r_mcangle_it 5.296 r_mcangle_other 5.294 r_scbond_other 4.183
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.496 r_dihedral_angle_3_deg 19.746 r_dihedral_angle_4_deg 11.755 r_long_range_B_other 8.378 r_long_range_B_refined 8.377 r_dihedral_angle_1_deg 7.397 r_scangle_other 6.383 r_mcangle_it 5.296 r_mcangle_other 5.294 r_scbond_other 4.183 r_scbond_it 4.181 r_mcbond_it 3.708 r_mcbond_other 3.699 r_angle_refined_deg 1.473 r_angle_other_deg 1.311 r_chiral_restr 0.057 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.003 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 2447 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing