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X-ray crystal structure of NapI L-arginine desaturase bound to Fe(II), L-arginine, and acetate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 7.5 293 potassium acetate, HEPES
Crystal Properties Matthews coefficient Solvent content 2.29 46.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.631 α = 90 b = 121.631 β = 90 c = 82.054 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 100 CCD MARMOSAIC 300 mm CCD 2014-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.979 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.1 50 99.6 0.116 0.122 0.038 7.2 10.2 40215
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 99.7 0.903 0.951 0.298 0.816 10
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 2.1 50 38124 2016 99.36 0.2048 0.2026 0.2078 0.2478 0.2547 RANDOM 33.734
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] -0.23 -0.12 -0.23 0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.679 r_dihedral_angle_4_deg 15.33 r_dihedral_angle_3_deg 12.06 r_dihedral_angle_1_deg 5.097 r_angle_refined_deg 0.943 r_angle_other_deg 0.701 r_chiral_restr 0.052 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.679 r_dihedral_angle_4_deg 15.33 r_dihedral_angle_3_deg 12.06 r_dihedral_angle_1_deg 5.097 r_angle_refined_deg 0.943 r_angle_other_deg 0.701 r_chiral_restr 0.052 r_bond_refined_d 0.005 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 5380 Nucleic Acid Atoms Solvent Atoms 287 Heterogen Atoms 42
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing