☰ Navigation Tabs
CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUINALDINE 2,4-DIOXYGENASE (HOD) CATALYTICALLY INACTIVE H251A VARIANT COMPLEXED WITH 2-METHYL- QUINOLIN-4(1H)-ONE UNDER HYPEROXIC CONDITIONS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7OJM
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 2.38 48.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.52 α = 90 b = 120.52 β = 90 c = 44.74 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 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 2.1 60.26 99.4 0.09 0.041 12.7 6.3 37761 28.1
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 2.1 2.16 0.758 0.487
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7OJM 2.101 60.26 37749 1793 99.358 0.192 0.1902 0.194 0.2284 0.2303 35.554
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] 0.72 0.72 -1.439
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.851 r_dihedral_angle_4_deg 16.592 r_dihedral_angle_3_deg 14.771 r_dihedral_angle_1_deg 6.449 r_lrange_it 5.821 r_lrange_other 5.733 r_scangle_it 3.865 r_scangle_other 3.865 r_mcangle_it 3.482 r_mcangle_other 3.482
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.851 r_dihedral_angle_4_deg 16.592 r_dihedral_angle_3_deg 14.771 r_dihedral_angle_1_deg 6.449 r_lrange_it 5.821 r_lrange_other 5.733 r_scangle_it 3.865 r_scangle_other 3.865 r_mcangle_it 3.482 r_mcangle_other 3.482 r_scbond_it 2.637 r_scbond_other 2.637 r_mcbond_it 2.414 r_mcbond_other 2.413 r_angle_refined_deg 1.324 r_angle_other_deg 1.212 r_nbd_other 0.296 r_symmetry_nbd_refined 0.266 r_metal_ion_refined 0.236 r_xyhbond_nbd_refined 0.216 r_nbd_refined 0.198 r_symmetry_nbd_other 0.191 r_symmetry_xyhbond_nbd_refined 0.167 r_nbtor_refined 0.16 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.064 r_ncsr_local_group_1 0.053 r_symmetry_xyhbond_nbd_other 0.043 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4461 Nucleic Acid Atoms Solvent Atoms 255 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing