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Crystal structure of 3-hydroxyanthranilate 3,4-dioxygenase from bovine kidney
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QNK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 298 40% (NH4)2SO4, Tris-HCl, 40mM MgCl2, 3% MPD, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.11 41.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.25 α = 91.7 b = 42.52 β = 113.3 c = 46.48 γ = 107.7
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 180 mm plate 1996-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.2 ELETTRA 5.2R
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 2.51 35.07 89.7 0.03 17.2 2.1 8486 8486
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) 2.51 2.58 60 0.041 3.1 2 183
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2QNK 2.51 35.07 8486 8486 399 89.67 0.16689 0.16312 0.1636 0.24031 0.2376 RANDOM 20.254
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] -0.47 -0.01 -0.24 0.12 0.05 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.183 r_dihedral_angle_3_deg 18.981 r_dihedral_angle_4_deg 18.289 r_dihedral_angle_1_deg 17.724 r_mcangle_it 2.088 r_scangle_it 1.94 r_angle_refined_deg 1.664 r_mcbond_it 1.253 r_scbond_it 1.199 r_nbtor_refined 0.333
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.183 r_dihedral_angle_3_deg 18.981 r_dihedral_angle_4_deg 18.289 r_dihedral_angle_1_deg 17.724 r_mcangle_it 2.088 r_scangle_it 1.94 r_angle_refined_deg 1.664 r_mcbond_it 1.253 r_scbond_it 1.199 r_nbtor_refined 0.333 r_symmetry_hbond_refined 0.291 r_nbd_refined 0.259 r_symmetry_vdw_refined 0.251 r_xyhbond_nbd_refined 0.207 r_chiral_restr 0.106 r_metal_ion_refined 0.038 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2270 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms 1
Software Software Software Name Purpose MAR345 data collection AMoRE phasing REFMAC refinement XDS data reduction