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Crystal structure kynurenine formamidase from Pseudomonas aeruginosa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R61 PDB ENTRY 1R61
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 293 0.1 M HEPES PH 7.5, 20 % (W/V) PEG [POLY(ETHYLENE GLYCOL)] 4000, AND 10 % (V/V) 2-PROPANOL. 293 K.
Crystal Properties Matthews coefficient Solvent content 2.41 49.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.721 α = 90 b = 112.721 β = 90 c = 90.761 γ = 120
Symmetry Space Group P 31 2 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 2013-05-03 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 2.37 28.9 99.2 0.06 16.8 4.9 27365
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 2.37 2.46 94.5 0.57 2.4 4.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1R61 2.37 97.62 25966 1377 99.16 0.15265 0.15047 0.19367 0.1891 RANDOM 50.986
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] 1.11 0.56 1.11 -3.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.184 r_dihedral_angle_4_deg 21.797 r_dihedral_angle_3_deg 15.147 r_scangle_it 7.734 r_dihedral_angle_1_deg 6.894 r_scbond_it 5.422 r_mcangle_it 5.228 r_mcbond_it 3.757 r_mcbond_other 3.749 r_angle_refined_deg 1.893
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.184 r_dihedral_angle_4_deg 21.797 r_dihedral_angle_3_deg 15.147 r_scangle_it 7.734 r_dihedral_angle_1_deg 6.894 r_scbond_it 5.422 r_mcangle_it 5.228 r_mcbond_it 3.757 r_mcbond_other 3.749 r_angle_refined_deg 1.893 r_angle_other_deg 0.898 r_symmetry_vdw_refined 0.383 r_symmetry_hbond_refined 0.3 r_nbd_refined 0.254 r_symmetry_vdw_other 0.199 r_nbd_other 0.198 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.103 r_nbtor_other 0.093 r_symmetry_hbond_other 0.086 r_bond_refined_d 0.018 r_xyhbond_nbd_other 0.016 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_metal_ion_refined 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 3158 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing