☰ 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 NORMOXIC CONDITIONS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CFS
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 = 119.19 α = 90 b = 119.19 β = 90 c = 44.44 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 2015-01-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91741 Diamond I04-1
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 44.44 99.3 0.108 0.05 10.5 6.4 42360 27.6
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 0.737 0.407 1.8
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 4CFS 2.001 42.14 42343 2116 99.243 0.206 0.2041 0.2066 0.2367 0.2398 32.536
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] 8.048 8.048 -16.096
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.832 r_dihedral_angle_4_deg 19.131 r_dihedral_angle_3_deg 15.157 r_dihedral_angle_1_deg 6.766 r_lrange_it 5.225 r_lrange_other 5.128 r_scangle_it 3.131 r_scangle_other 3.131 r_mcangle_it 3.12 r_mcangle_other 3.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.832 r_dihedral_angle_4_deg 19.131 r_dihedral_angle_3_deg 15.157 r_dihedral_angle_1_deg 6.766 r_lrange_it 5.225 r_lrange_other 5.128 r_scangle_it 3.131 r_scangle_other 3.131 r_mcangle_it 3.12 r_mcangle_other 3.12 r_mcbond_it 2.133 r_mcbond_other 2.133 r_scbond_it 2.097 r_scbond_other 2.097 r_angle_refined_deg 1.335 r_angle_other_deg 1.183 r_nbd_other 0.296 r_symmetry_nbd_refined 0.244 r_metal_ion_refined 0.242 r_xyhbond_nbd_refined 0.217 r_nbd_refined 0.206 r_symmetry_nbd_other 0.193 r_symmetry_xyhbond_nbd_refined 0.17 r_nbtor_refined 0.161 r_symmetry_xyhbond_nbd_other 0.126 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.064 r_ncsr_local_group_1 0.028 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4444 Nucleic Acid Atoms Solvent Atoms 244 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing