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Aeromonas caviae CMP-Pse5A7Ac Synthetase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold Q2M5Q2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 1% w/v Tryptone, 0.05 M HEPES sodium pH 6.5, 14% w/v PEG3350, 0.001 M sodium azide
Crystal Properties Matthews coefficient Solvent content 2.69 54.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.527 α = 90 b = 109.527 β = 90 c = 87.063 γ = 120
Symmetry Space Group P 65 2 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 PIXEL DECTRIS EIGER2 S 16M 2022-05-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976 Diamond I03
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 1.9 64.223 100 0.218 0.223 0.048 0.999 14.8 40 24845
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 1.9 1.94 4.346 4.447 0.943 0.917 41.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.9 64.223 24803 1187 99.984 0.194 0.1916 0.1899 0.2406 0.2361 39.633
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] 0.476 0.238 0.476 -1.544
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.79 r_dihedral_angle_3_deg 15.513 r_lrange_it 7.733 r_lrange_other 7.71 r_dihedral_angle_1_deg 7.106 r_dihedral_angle_2_deg 6.83 r_scangle_it 5.824 r_scangle_other 5.822 r_mcangle_it 4.124 r_mcangle_other 4.123
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.79 r_dihedral_angle_3_deg 15.513 r_lrange_it 7.733 r_lrange_other 7.71 r_dihedral_angle_1_deg 7.106 r_dihedral_angle_2_deg 6.83 r_scangle_it 5.824 r_scangle_other 5.822 r_mcangle_it 4.124 r_mcangle_other 4.123 r_scbond_it 4.037 r_scbond_other 4.035 r_mcbond_it 3.008 r_mcbond_other 3.008 r_angle_refined_deg 2.174 r_angle_other_deg 0.717 r_nbd_refined 0.226 r_symmetry_nbd_other 0.209 r_nbtor_refined 0.193 r_nbd_other 0.183 r_xyhbond_nbd_refined 0.18 r_chiral_restr 0.108 r_symmetry_xyhbond_nbd_refined 0.107 r_symmetry_nbtor_other 0.09 r_symmetry_nbd_refined 0.08 r_symmetry_xyhbond_nbd_other 0.047 r_bond_refined_d 0.016 r_gen_planes_refined 0.014 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1827 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction