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N(5)-hydroxyornithine:cis-anhydromevalonyl coenzyme A-N(5)-transacylase sidF N-terminal domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-Q4QF55-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 293 0.2M potassium sodium tartrate tetrahydrate, 20% w/v polyethylene glycol 3350, cryoprotected with 40% Morpheus precipitant mix 3
Crystal Properties Matthews coefficient Solvent content 2.68 54.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.2 α = 90 b = 110.67 β = 90 c = 69.474 γ = 90
Symmetry Space Group C 2 2 21
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 PILATUS 6M 2022-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.58 29.438 99.8 0.998 4.4 12.2 7832 49.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.58 2.7 99.2 0.942 4.4 12.3
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.581 29.438 7818 367 99.783 0.176 0.1726 0.1727 0.236 0.2356 random 51.123
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] -0.242 1.351 -1.109
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.156 r_dihedral_angle_6_deg 15.708 r_dihedral_angle_2_deg 14.913 r_lrange_other 13.935 r_lrange_it 13.927 r_scangle_it 11.835 r_scangle_other 11.829 r_mcangle_other 9.785 r_mcangle_it 9.771 r_scbond_it 9.052
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.156 r_dihedral_angle_6_deg 15.708 r_dihedral_angle_2_deg 14.913 r_lrange_other 13.935 r_lrange_it 13.927 r_scangle_it 11.835 r_scangle_other 11.829 r_mcangle_other 9.785 r_mcangle_it 9.771 r_scbond_it 9.052 r_scbond_other 9.046 r_dihedral_angle_1_deg 8.422 r_mcbond_other 7.485 r_mcbond_it 7.484 r_angle_refined_deg 2.192 r_angle_other_deg 0.834 r_nbd_refined 0.22 r_nbtor_refined 0.189 r_symmetry_nbd_other 0.178 r_xyhbond_nbd_refined 0.161 r_symmetry_xyhbond_nbd_refined 0.14 r_nbd_other 0.106 r_chiral_restr 0.1 r_symmetry_nbd_refined 0.093 r_symmetry_nbtor_other 0.086 r_gen_planes_refined 0.014 r_bond_refined_d 0.013 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1376 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MrBUMP phasing