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CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUINALDINE 2,4-DIOXYGENASE (HOD) FROM ARTHROBACTER NITROGUAJACOLICUS RU61A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other HOD H251A MUTANT SOLVED BY SAD IN SPACE GROUP P 43 21 2 AND NOT FULLY REFINED
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 HIS6-HOD AT 150 MG/ML IN STORAGE BUFFER IN THE PRESENCE OF A RESERVOIR COMPOSED OF 1.65 M SODIUM/POTASSIUM TARTRATE, 0.1 M HEPES PH 7.0
Crystal Properties Matthews coefficient Solvent content 2.44 49.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.17 α = 90 b = 167.86 β = 90 c = 168.03 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 CCD ADSC CCD MIRRORS 2009-01-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.09 53.15 99.6 0.07 11.8 4.4 75553 41.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.09 2.21 100 0.47 5.3 4.4
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT HOD H251A MUTANT SOLVED BY SAD IN SPACE GROUP P 43 21 2 AND NOT FULLY REFINED 2.09 53.16 71190 3878 97.5 0.198 0.196 0.2059 0.232 TWIN LAW TAKEN INTO ACCOUNT 32.15
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] 1.99 -5.7 3.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.133 r_dihedral_angle_4_deg 19.457 r_dihedral_angle_3_deg 15.687 r_dihedral_angle_1_deg 6.464 r_scangle_it 2.898 r_scbond_it 1.872 r_angle_refined_deg 1.528 r_mcangle_it 1.107 r_angle_other_deg 1.02 r_mcbond_it 0.624
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.133 r_dihedral_angle_4_deg 19.457 r_dihedral_angle_3_deg 15.687 r_dihedral_angle_1_deg 6.464 r_scangle_it 2.898 r_scbond_it 1.872 r_angle_refined_deg 1.528 r_mcangle_it 1.107 r_angle_other_deg 1.02 r_mcbond_it 0.624 r_mcbond_other 0.208 r_chiral_restr 0.092 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8921 Nucleic Acid Atoms Solvent Atoms 279 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing