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Crystal structure of CbFMN4 domain 1
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, SITTING DROP 7.7 294 3.4 M ammonium sulfate, 0.1 M bis-tris-propane
Crystal Properties Matthews coefficient Solvent content 3.4 63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.915 α = 90 b = 124.915 β = 90 c = 29.846 γ = 120
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 2022-08-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.9655 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 2.6 40.9 100 0.152 0.161 0.052 0.998 13.7 9.7 8547
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 2.6 2.72 100 2.623 2.773 0.894 0.526 9.5
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.6 40.9 8151 388 99.93 0.18378 0.18212 0.21917 0.1759 RANDOM 62.6
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] -1.73 -0.86 -1.73 5.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.702 r_long_range_B_refined 8.86 r_long_range_B_other 8.857 r_dihedral_angle_2_deg 7.846 r_dihedral_angle_1_deg 7.425 r_scangle_other 7.23 r_mcangle_other 6.838 r_mcangle_it 6.825 r_scbond_it 4.879 r_scbond_other 4.864
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.702 r_long_range_B_refined 8.86 r_long_range_B_other 8.857 r_dihedral_angle_2_deg 7.846 r_dihedral_angle_1_deg 7.425 r_scangle_other 7.23 r_mcangle_other 6.838 r_mcangle_it 6.825 r_scbond_it 4.879 r_scbond_other 4.864 r_mcbond_it 4.587 r_mcbond_other 4.439 r_angle_refined_deg 1.377 r_angle_other_deg 0.463 r_chiral_restr 0.055 r_bond_refined_d 0.007 r_gen_planes_refined 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 1230 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction