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Crystal structure of kynurenine formamidase from Burkholderia cenocepacia
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other KYNURENINE FORMAMIDASE FROM PSEUDOMONAS AERUGINOSA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 293 14 % (W/V) PEG 3350, 5 MM COCL2, 5 MM CDCL2, 5 MM MGCL2 AND 5 MM NICL2. 293 K.
Crystal Properties Matthews coefficient Solvent content 2.26 45.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.859 α = 90 b = 50.12 β = 94.15 c = 135.197 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 2012-09-23 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 1.6 28.37 99.3 0.07 12.8 3.6 134904
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 1.6 1.69 99.8 0.48 3 3.6
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 KYNURENINE FORMAMIDASE FROM PSEUDOMONAS AERUGINOSA 1.6 134.84 128111 6778 99.21 0.15063 0.14886 0.1484 0.18431 0.1837 RANDOM 18.874
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] -0.19 -0.04 0.28 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.829 r_dihedral_angle_4_deg 18.843 r_dihedral_angle_3_deg 12.653 r_dihedral_angle_1_deg 6.21 r_scangle_it 3.639 r_mcangle_it 2.684 r_scbond_it 2.601 r_angle_refined_deg 2.422 r_mcbond_it 1.834 r_metal_ion_refined 0.537
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.829 r_dihedral_angle_4_deg 18.843 r_dihedral_angle_3_deg 12.653 r_dihedral_angle_1_deg 6.21 r_scangle_it 3.639 r_mcangle_it 2.684 r_scbond_it 2.601 r_angle_refined_deg 2.422 r_mcbond_it 1.834 r_metal_ion_refined 0.537 r_nbtor_refined 0.316 r_symmetry_vdw_refined 0.308 r_nbd_refined 0.26 r_chiral_restr 0.221 r_xyhbond_nbd_refined 0.145 r_symmetry_hbond_refined 0.1 r_bond_refined_d 0.025 r_gen_planes_refined 0.014 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other 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_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 6212 Nucleic Acid Atoms Solvent Atoms 1068 Heterogen Atoms 131
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing