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NifS soaked with(2R,3R)-3-ethoxycarbonylaziridine-2-carboxylic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5WT2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 85 mM HEPES/NaOH, 17%(w/v) PEG4000, 15%(v/v) glycerol, 8.5% (v/v) isopropanol
Crystal Properties Matthews coefficient Solvent content 4.02 69.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.18 α = 90 b = 103.18 β = 90 c = 133.35 γ = 90
Symmetry Space Group P 41 21 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 2021-12-05 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 2.8 50 99.9 0.094 0.999 19.58 12.9 18331
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 2.8 2.9 99.9 0.927 0.962 3.57 13.8
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 5WT2 2.8 48.11 17412 917 99.92 0.2053 0.20325 0.2055 0.24285 0.2455 RANDOM 99.285
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] -3.17 -3.17 6.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.201 r_long_range_B_refined 14.795 r_dihedral_angle_2_deg 8.541 r_mcangle_it 7.889 r_dihedral_angle_1_deg 7.208 r_scbond_it 5.548 r_mcbond_it 4.949 r_angle_refined_deg 2.058 r_chiral_restr 0.167 r_gen_planes_refined 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.201 r_long_range_B_refined 14.795 r_dihedral_angle_2_deg 8.541 r_mcangle_it 7.889 r_dihedral_angle_1_deg 7.208 r_scbond_it 5.548 r_mcbond_it 4.949 r_angle_refined_deg 2.058 r_chiral_restr 0.167 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 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 2817 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data reduction PHASER phasing