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Crystal structure of SaFMN3 domain 2
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 294 38 - 42 % PEG3350, 0.05 M bis-tris
Crystal Properties Matthews coefficient Solvent content 1.9 35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 25.954 α = 90 b = 25.954 β = 90 c = 364.838 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 PILATUS3 6M 2022-04-22 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 45.6 100 0.14 0.146 0.039 0.996 9 13.1 5999
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 2.05 100 0.452 0.473 0.137 0.982 11
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 2 30.42 5592 260 99.98 0.23395 0.23097 0.2404 0.29763 0.3119 RANDOM 46.793
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] 0.28 0.14 0.28 -0.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.203 r_dihedral_angle_3_deg 16.228 r_dihedral_angle_1_deg 7.062 r_long_range_B_refined 5.224 r_long_range_B_other 5.19 r_scangle_other 2.907 r_mcangle_it 2.463 r_mcangle_other 2.461 r_scbond_it 2.192 r_scbond_other 2.121
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.203 r_dihedral_angle_3_deg 16.228 r_dihedral_angle_1_deg 7.062 r_long_range_B_refined 5.224 r_long_range_B_other 5.19 r_scangle_other 2.907 r_mcangle_it 2.463 r_mcangle_other 2.461 r_scbond_it 2.192 r_scbond_other 2.121 r_mcbond_it 1.73 r_mcbond_other 1.729 r_angle_refined_deg 1.51 r_angle_other_deg 0.474 r_chiral_restr 0.064 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 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 627 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction