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Crystal structure of Fic25 (holo form) from Streptomyces ficellus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8GYH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293.15 1.0 M Sodium citrate, 0.1 M Imidazole, pH 8.0
Crystal Properties Matthews coefficient Solvent content 3.57 65.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 201.628 α = 90 b = 201.628 β = 90 c = 57.009 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 2021-12-11 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 1.93 48.48 99.5 0.12 0.998 17.3 10.2 99447
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 1.93 1.96 0.9 0.817 2.8
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 8GYH 1.93 48.48 94493 4946 99.45 0.1677 0.1666 0.1762 0.1878 0.1991 RANDOM 24.539
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] 0.71 0.35 0.71 -2.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.074 r_dihedral_angle_4_deg 15.725 r_dihedral_angle_3_deg 13.209 r_dihedral_angle_1_deg 6.026 r_angle_refined_deg 1.244 r_angle_other_deg 1.165 r_chiral_restr 0.049 r_bond_refined_d 0.018 r_gen_planes_refined 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.074 r_dihedral_angle_4_deg 15.725 r_dihedral_angle_3_deg 13.209 r_dihedral_angle_1_deg 6.026 r_angle_refined_deg 1.244 r_angle_other_deg 1.165 r_chiral_restr 0.049 r_bond_refined_d 0.018 r_gen_planes_refined 0.004 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 755 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction