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Crystal structure of kynurenine formamidase from Bacillus anthracis complexed with 2-aminoacetophenone.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CO9 PDB ENTRY 4CO9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 293 100 MM TRIS-HCL PH 8.5, 140 MM MGCL2 AND 30 % (W/V) PEG 4000. 293 K. PROTEIN WAS PREVIOUSLY INCUBATED WITH 5 % (V/V) 2-AMINOACETOPHENONE.
Crystal Properties Matthews coefficient Solvent content 2.23 44.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.695 α = 90 b = 66.561 β = 90.24 c = 84.061 γ = 90
Symmetry Space Group P 1 21 1
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 PILATUS 6M MIRRORS 2013-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.25 42.64 98.1 0.16 4.8 2.7 38046
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.32 97.7 0.55 2.2 2.7
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 PDB ENTRY 4CO9 2.24 42.64 36106 1916 96.69 0.18576 0.1837 0.1869 0.2241 0.2245 RANDOM 20.693
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] 7.17 6.27 5.74 -12.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.668 r_dihedral_angle_3_deg 14.365 r_dihedral_angle_4_deg 12.657 r_dihedral_angle_1_deg 6.727 r_scangle_it 3.963 r_mcangle_it 3.09 r_scbond_it 2.495 r_mcbond_it 2.008 r_mcbond_other 2.006 r_angle_refined_deg 1.684
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.668 r_dihedral_angle_3_deg 14.365 r_dihedral_angle_4_deg 12.657 r_dihedral_angle_1_deg 6.727 r_scangle_it 3.963 r_mcangle_it 3.09 r_scbond_it 2.495 r_mcbond_it 2.008 r_mcbond_other 2.006 r_angle_refined_deg 1.684 r_angle_other_deg 1.343 r_symmetry_hbond_refined 0.509 r_symmetry_vdw_refined 0.312 r_nbd_refined 0.238 r_metal_ion_refined 0.205 r_symmetry_vdw_other 0.198 r_nbd_other 0.197 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.163 r_symmetry_hbond_other 0.145 r_xyhbond_nbd_other 0.132 r_chiral_restr 0.1 r_nbtor_other 0.088 r_bond_refined_d 0.017 r_gen_planes_refined 0.012 r_bond_other_d 0.009 r_gen_planes_other 0.008 r_metal_ion_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined 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 6467 Nucleic Acid Atoms Solvent Atoms 412 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing