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Aeromonas caviae CMP-Pse5Ac7Ac synthetase in the presence of CMP-Pse5Ac7Ac.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Apo model (to be deposited)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291.15 0.2 M Sodium Nitrate; 0.1 M Bis-Tris Propane pH 6.5; 24% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.22 44.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.574 α = 90 b = 79.007 β = 92.46 c = 74.039 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 X 16M 2024-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9537 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.5 54 99.7 0.039 0.054 0.037 0.997 15 3.5 78069
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 0.106 0.146 0.1 0.975 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.5 42.571 78042 4148 99.65 0.168 0.1668 0.1854 0.2072 15.153
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] 0.012 -0.16 0.814 -0.809
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.795 r_dihedral_angle_3_deg 12.307 r_dihedral_angle_1_deg 6.295 r_dihedral_angle_2_deg 6.154 r_lrange_it 6.11 r_lrange_other 5.927 r_scangle_it 4.089 r_scangle_other 4.088 r_dihedral_angle_other_2_deg 3.949 r_scbond_it 2.681
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.795 r_dihedral_angle_3_deg 12.307 r_dihedral_angle_1_deg 6.295 r_dihedral_angle_2_deg 6.154 r_lrange_it 6.11 r_lrange_other 5.927 r_scangle_it 4.089 r_scangle_other 4.088 r_dihedral_angle_other_2_deg 3.949 r_scbond_it 2.681 r_scbond_other 2.68 r_mcangle_it 2.6 r_mcangle_other 2.6 r_mcbond_it 1.756 r_mcbond_other 1.75 r_angle_refined_deg 1.729 r_angle_other_deg 0.57 r_symmetry_xyhbond_nbd_refined 0.378 r_nbd_other 0.261 r_nbd_refined 0.224 r_symmetry_nbd_refined 0.199 r_symmetry_nbd_other 0.187 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.123 r_chiral_restr 0.086 r_symmetry_nbtor_other 0.08 r_symmetry_xyhbond_nbd_other 0.058 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3596 Nucleic Acid Atoms Solvent Atoms 416 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction