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NifS with L-penicillamine
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 3.96 68.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.936 α = 90 b = 102.936 β = 90 c = 132.067 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 PILATUS3 S 2M 2021-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.000 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 3 48.91 99.9 0.074 0.077 1 27.43 12.75 14795 82.48
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.1 100 0.886 0.923 0.932 3.22 12.936
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 3 48.91 14055 740 99.95 0.1735 0.1713 0.1731 0.2153 0.2176 RANDOM 114.128
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] -1.56 -1.56 3.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.052 r_dihedral_angle_3_deg 22.808 r_dihedral_angle_4_deg 16.817 r_dihedral_angle_1_deg 7.966 r_angle_refined_deg 2.216 r_chiral_restr 0.156 r_bond_refined_d 0.011 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2755 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms 29
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing