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ROOM TEMPERATURE CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUINALDINE 2,4-DIOXYGENASE (HOD) UNDER XENON PRESSURE (30 bar)
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 2 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 2.42 48.22 48.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.86 α = 90 b = 169.46 β = 90 c = 169.31 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 2 x-ray 293 PIXEL DECTRIS PILATUS 6M 2012-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.96860 Diamond I24
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 2.897 53.583 99.2 0.198 0.061 5.4 4.4 29421 59.9
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 2.897 2.95 95.8 1.12 0.623 1.3
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2WJ3 2.897 53.583 29381 1483 98.806 0.193 0.1918 0.2203 0.2486 62.756
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] 3.482 0.271 -3.753
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.004 r_dihedral_angle_4_deg 15.607 r_dihedral_angle_3_deg 14.172 r_lrange_it 7.364 r_lrange_other 7.364 r_dihedral_angle_1_deg 5.964 r_mcangle_it 4.336 r_mcangle_other 4.336 r_scangle_it 3.91 r_scangle_other 3.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.004 r_dihedral_angle_4_deg 15.607 r_dihedral_angle_3_deg 14.172 r_lrange_it 7.364 r_lrange_other 7.364 r_dihedral_angle_1_deg 5.964 r_mcangle_it 4.336 r_mcangle_other 4.336 r_scangle_it 3.91 r_scangle_other 3.91 r_mcbond_it 2.672 r_mcbond_other 2.672 r_scbond_it 2.375 r_scbond_other 2.375 r_angle_other_deg 1.448 r_angle_refined_deg 1.312 r_nbd_other 0.269 r_symmetry_nbd_refined 0.208 r_nbd_refined 0.202 r_symmetry_nbd_other 0.176 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.127 r_chiral_restr 0.081 r_symmetry_nbtor_other 0.08 r_symmetry_xyhbond_nbd_refined 0.059 r_ncsr_local_group_4 0.039 r_ncsr_local_group_1 0.035 r_ncsr_local_group_6 0.032 r_ncsr_local_group_5 0.029 r_ncsr_local_group_2 0.027 r_ncsr_local_group_3 0.022 r_ext_dist_refined_d 0.01 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8966 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling REFMAC phasing