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Crystal structure of Fic25 (apo form) from Streptomyces ficellus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold Model constructed by AlphaFold2 from the primary amino acid sequence of Fic25
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 1.0 M Sodium citrate, 0.1 M Imidazole, pH8.0
Crystal Properties Matthews coefficient Solvent content 3.57 65.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 201.658 α = 90 b = 201.658 β = 90 c = 56.992 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 95 PIXEL DECTRIS PILATUS3 6M 2021-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.8 48.484 100 0.112 0.999 18.9 10.2 122992
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.83 0.94 0.835
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 Model constructed by AlphaFold2 from the primary amino acid sequence of Fic25 1.8 48.48 116639 6325 99.96 0.172 0.171 0.1817 0.1914 0.1987 RANDOM 21.536
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] 0.72 0.36 0.72 -2.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.19 r_dihedral_angle_1_deg 5.75 r_dihedral_angle_2_deg 4.485 r_angle_refined_deg 0.932 r_angle_other_deg 0.322 r_chiral_restr 0.045 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6299 Nucleic Acid Atoms Solvent Atoms 745 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PDB_EXTRACT data extraction PHASER phasing