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CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUINALDINE 2,4-DIOXYGENASE (HOD) S101A VARIANT COMPLEXED WITH 2-METHYL-QUINOLIN-4(1H)-ONE UNDER NORMOXYC CONDITIONS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WJ4
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 2.37 48.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.8 α = 90 b = 167.79 β = 90 c = 167.91 γ = 90
Symmetry Space Group P 21 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 PIXEL DECTRIS PILATUS 6M-F 2015-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97949 Diamond I02
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 46.56 99.8 0.092 0.04 12.7 7.1 86750
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 98.5 0.866 0.375 2.3
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 (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 46.56 86659 4298 99.82 0.174 0.1734 0.178 0.1942 0.1986 33.936
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] -16.477 8.801 7.676
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.358 r_dihedral_angle_4_deg 18.281 r_dihedral_angle_3_deg 14.648 r_dihedral_angle_1_deg 6.615 r_lrange_it 5.625 r_lrange_other 5.624 r_scangle_it 4.077 r_scangle_other 4.077 r_mcangle_it 3.745 r_mcangle_other 3.745
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.358 r_dihedral_angle_4_deg 18.281 r_dihedral_angle_3_deg 14.648 r_dihedral_angle_1_deg 6.615 r_lrange_it 5.625 r_lrange_other 5.624 r_scangle_it 4.077 r_scangle_other 4.077 r_mcangle_it 3.745 r_mcangle_other 3.745 r_scbond_it 2.8 r_scbond_other 2.8 r_mcbond_it 2.662 r_mcbond_other 2.661 r_angle_refined_deg 1.336 r_angle_other_deg 1.213 r_symmetry_nbd_refined 0.401 r_nbd_other 0.351 r_symmetry_xyhbond_nbd_refined 0.252 r_nbd_refined 0.193 r_symmetry_nbd_other 0.184 r_xyhbond_nbd_refined 0.174 r_nbtor_refined 0.162 r_symmetry_xyhbond_nbd_other 0.14 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.067 r_ncsr_local_group_4 0.034 r_ncsr_local_group_6 0.033 r_ncsr_local_group_2 0.032 r_ncsr_local_group_3 0.032 r_ncsr_local_group_5 0.031 r_ncsr_local_group_1 0.027 r_bond_refined_d 0.006 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 8904 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing