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CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUINALDINE 2,4-DIOXYGENASE (HOD) H251A VARIANT COMPLEXED WITH N-ACETYLANTHRANILATE AS RESULT OF IN CRYSTALLO TURNOVER OF ITS NATURAL SUBSTRATE 1-H-3-HYDROXY-4- OXOQUINALDINE UNDER HYPEROXIC CONDITIONS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WJ3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 293 PROTEIN AT 150 MG/ML IN STORAGE BUFFER 1.65M NA/K TARTRATE, 0.1M HEPES PH 7.0
Crystal Properties Matthews coefficient Solvent content 2.41 49.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.06 α = 90 b = 120.06 β = 90 c = 44.5 γ = 90
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 2014-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.97981 ESRF BM30A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 29.12 97.9 0.074 0.033 20.1 6.9 42489
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 89.9 0.639 0.535 1.4
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.003 29.12 37765 1910 87.421 0.205 0.203 0.207 0.2355 0.2387 26.706
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] 0.683 0.683 -1.365
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.939 r_dihedral_angle_3_deg 16.855 r_dihedral_angle_4_deg 16.759 r_dihedral_angle_1_deg 6.961 r_lrange_it 4.657 r_lrange_other 4.599 r_scangle_it 2.708 r_scangle_other 2.708 r_mcangle_it 2.703 r_mcangle_other 2.701
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.939 r_dihedral_angle_3_deg 16.855 r_dihedral_angle_4_deg 16.759 r_dihedral_angle_1_deg 6.961 r_lrange_it 4.657 r_lrange_other 4.599 r_scangle_it 2.708 r_scangle_other 2.708 r_mcangle_it 2.703 r_mcangle_other 2.701 r_mcbond_it 1.863 r_mcbond_other 1.862 r_scbond_it 1.825 r_scbond_other 1.825 r_angle_refined_deg 1.387 r_angle_other_deg 1.203 r_symmetry_nbd_refined 0.438 r_nbd_other 0.428 r_nbd_refined 0.223 r_symmetry_xyhbond_nbd_refined 0.212 r_symmetry_nbd_other 0.191 r_xyhbond_nbd_refined 0.188 r_metal_ion_refined 0.175 r_nbtor_refined 0.162 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.066 r_ncsr_local_group_1 0.045 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4440 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 82
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing