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FSP1 (tetrapod ancestor) bound to FAD and NAD+ and compound 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9IFT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.06 M MgCl2, CaCl2, 0.1M imidazole/MES monohydrate (acid) pH 6.5, 12.5% MPD, 12.5% PEG1000, 12.5% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.44 49.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.567 α = 90 b = 79.684 β = 98.61 c = 113.062 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 PILATUS3 6M 2024-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.965459 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.55 64.97 83.7 0.106 0.133 0.079 5.1 2.5 46979
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.551 1.842 5.3 0.393 0.484 0.279 2.6
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 1.55 64.97 44700 2279 42.51 0.18222 0.17919 0.188 0.24249 0.2455 RANDOM 19.923
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] 0.08 -0.14 0.06 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.378 r_dihedral_angle_3_deg 14.12 r_dihedral_angle_1_deg 6.995 r_long_range_B_refined 6.438 r_long_range_B_other 6.387 r_scangle_other 4.31 r_mcangle_it 2.785 r_mcangle_other 2.785 r_scbond_it 2.567 r_scbond_other 2.567
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.378 r_dihedral_angle_3_deg 14.12 r_dihedral_angle_1_deg 6.995 r_long_range_B_refined 6.438 r_long_range_B_other 6.387 r_scangle_other 4.31 r_mcangle_it 2.785 r_mcangle_other 2.785 r_scbond_it 2.567 r_scbond_other 2.567 r_mcbond_it 1.727 r_mcbond_other 1.726 r_angle_refined_deg 1.341 r_angle_other_deg 0.439 r_chiral_restr 0.06 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 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 5544 Nucleic Acid Atoms Solvent Atoms 556 Heterogen Atoms 258
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing