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FAD-dependent monooxygenase sorC with sorbicillin bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.2 M ammonium citrate dibasic, 20% PEG3350, 1 mM sorbicillin, 1 mM NAD+
Crystal Properties Matthews coefficient Solvent content 1.89 34.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.321 α = 90 b = 90.965 β = 90 c = 94.552 γ = 90
Symmetry Space Group P 21 21 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 PILATUS3 6M 2024-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.96546 ESRF MASSIF-1
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 1.71 42.32 96.4 0.053 0.06 0.028 0.999 13.1 4.3 38849
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 1.71 1.74 86.8 1.019 1.163 0.547 0.528 4.1
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 (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 1.71 38.66 36899 1916 95.69 0.17494 0.17237 0.1839 0.22737 0.235 RANDOM 26.736
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] -0.03 -0.11 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.126 r_dihedral_angle_3_deg 11.242 r_dihedral_angle_1_deg 6.344 r_long_range_B_other 6.308 r_long_range_B_refined 6.297 r_scangle_other 4.765 r_mcangle_it 3.371 r_mcangle_other 3.371 r_scbond_it 3.213 r_scbond_other 3.199
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.126 r_dihedral_angle_3_deg 11.242 r_dihedral_angle_1_deg 6.344 r_long_range_B_other 6.308 r_long_range_B_refined 6.297 r_scangle_other 4.765 r_mcangle_it 3.371 r_mcangle_other 3.371 r_scbond_it 3.213 r_scbond_other 3.199 r_mcbond_it 2.421 r_mcbond_other 2.4 r_angle_refined_deg 1.618 r_angle_other_deg 0.561 r_chiral_restr 0.078 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 3215 Nucleic Acid Atoms Solvent Atoms 259 Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction