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Crystal structure of BioU from Synechocystis sp.PCC6803 conjugated with DAPA
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 18% (w/v) PEG 3350, 0.2M potassium formate, 0.21M HEPES-NaOH (pH7.0)
Crystal Properties Matthews coefficient Solvent content 1.89 35.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.114 α = 90 b = 71.114 β = 90 c = 98.198 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 PIXEL DECTRIS PILATUS 2M 2018-11-28 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) 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 2.3 50 99.9 0.086 0.031 0.992 29.4 8.8 13306
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 2.3 2.34 0.604 0.211 0.88
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 2.3 30.81 12589 695 99.83 0.19998 0.19557 0.1972 0.2782 0.2737 RANDOM 53.443
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] 0.29 0.15 0.29 -0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.044 r_dihedral_angle_3_deg 18.332 r_dihedral_angle_4_deg 15.349 r_long_range_B_refined 9.392 r_long_range_B_other 9.39 r_scangle_other 7.386 r_dihedral_angle_1_deg 7.377 r_mcangle_it 6.124 r_mcangle_other 6.124 r_scbond_it 4.906
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.044 r_dihedral_angle_3_deg 18.332 r_dihedral_angle_4_deg 15.349 r_long_range_B_refined 9.392 r_long_range_B_other 9.39 r_scangle_other 7.386 r_dihedral_angle_1_deg 7.377 r_mcangle_it 6.124 r_mcangle_other 6.124 r_scbond_it 4.906 r_scbond_other 4.904 r_mcbond_it 4.233 r_mcbond_other 4.228 r_angle_refined_deg 1.5 r_angle_other_deg 1.357 r_chiral_restr 0.065 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 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 2437 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing