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Pyrococcus furiosus FdxA D14H variant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SJ1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M tri-lithium citrate, 20% (w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 2.47 50.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.88 α = 90 b = 77.88 β = 90 c = 40.66 γ = 120
Symmetry Space Group P 61 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 EIGER X 16M 2023-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.3 50 99.4 0.074 0.999 21.35 17.9 3492
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.4 99.8 1.07 0.958 3.79 18
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 1SJ1 2.3 38.94 3316 175 99.4 0.19393 0.19091 0.1897 0.24454 0.2433 RANDOM 85.005
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] 2.37 1.19 2.37 -7.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 51.153 r_dihedral_angle_3_deg 24.632 r_long_range_B_refined 14.031 r_scbond_it 7.212 r_mcangle_it 7.148 r_dihedral_angle_1_deg 6.953 r_mcbond_it 5.097 r_angle_refined_deg 3.174 r_chiral_restr 0.223 r_bond_refined_d 0.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 51.153 r_dihedral_angle_3_deg 24.632 r_long_range_B_refined 14.031 r_scbond_it 7.212 r_mcangle_it 7.148 r_dihedral_angle_1_deg 6.953 r_mcbond_it 5.097 r_angle_refined_deg 3.174 r_chiral_restr 0.223 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 498 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing