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Structure of 2,5-dihydroxypridine Dioxygenase from Pseudomonas putida KT2440 in complex with product N-formylmaleamic acid formed via in crystallo reaction with 2,5-dihydroxypridine
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2M Succnic acid PH7 20%PEG3350
Crystal Properties Matthews coefficient Solvent content 2.33 47.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.885 α = 90 b = 125.916 β = 90 c = 144.129 γ = 90
Symmetry Space Group P 2 21 21
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 ADSC QUANTUM 315r 2018-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9789 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.28 50 99.2 0.101 8.7 6 98134
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.28 2.4 0.711 3
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 SAD THROUGHOUT 2.28 30 93165 4901 98.99 0.2135 0.2106 0.2196 0.2673 0.2695 RANDOM 67.306
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] -3.2 -3.51 6.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.51 r_dihedral_angle_4_deg 19.142 r_dihedral_angle_3_deg 15.101 r_dihedral_angle_1_deg 6.754 r_angle_other_deg 3.635 r_angle_refined_deg 1.644 r_chiral_restr 0.09 r_bond_refined_d 0.014 r_gen_planes_other 0.01 r_gen_planes_refined 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.51 r_dihedral_angle_4_deg 19.142 r_dihedral_angle_3_deg 15.101 r_dihedral_angle_1_deg 6.754 r_angle_other_deg 3.635 r_angle_refined_deg 1.644 r_chiral_restr 0.09 r_bond_refined_d 0.014 r_gen_planes_other 0.01 r_gen_planes_refined 0.008 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16338 Nucleic Acid Atoms Solvent Atoms 241 Heterogen Atoms 6
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction PHASER phasing