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Crystal structure of BioU (H233A) 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 20% PEG 3350, 0.2M Ammonium fluoride
Crystal Properties Matthews coefficient Solvent content 1.92 35.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.425 α = 90 b = 71.425 β = 90 c = 98.511 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 2018-12-08 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 1.78 50 100 0.1 0.034 0.993 33.8 9.5 28597
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 1.78 1.81 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 1.78 38.56 27115 1447 99.95 0.1949 0.19216 0.2014 0.24831 0.2538 RANDOM 32.713
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] -0.22 -0.11 -0.22 0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.393 r_dihedral_angle_4_deg 18.292 r_dihedral_angle_3_deg 16.235 r_dihedral_angle_1_deg 6.838 r_long_range_B_refined 5.931 r_long_range_B_other 5.909 r_scangle_other 4.663 r_mcangle_it 3.212 r_mcangle_other 3.212 r_scbond_it 2.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.393 r_dihedral_angle_4_deg 18.292 r_dihedral_angle_3_deg 16.235 r_dihedral_angle_1_deg 6.838 r_long_range_B_refined 5.931 r_long_range_B_other 5.909 r_scangle_other 4.663 r_mcangle_it 3.212 r_mcangle_other 3.212 r_scbond_it 2.96 r_scbond_other 2.959 r_mcbond_it 2.345 r_mcbond_other 2.344 r_angle_other_deg 1.479 r_angle_refined_deg 1.476 r_chiral_restr 0.077 r_bond_refined_d 0.007 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 2446 Nucleic Acid Atoms Solvent Atoms 164 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing