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Crystal Structure of Xanthine Dehydrogenase (E232Q variant) from Rhodobacter capsulatus in Complex with Hypoxanthine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JRO PDB ENTRY 1JRO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.3 100 MM TRIS PH 8.3, 6-8 % PEG 8000, 6-8 MM BACL, 5-25 MM DTT, 3-4 % ISOPROPANOL, 10-15 MG/ML PROTEIN IN A 1:2 RATIO WITH THE RESERVOIR SOLUTION, HANGING DROP VAPOR DIFFUSION
Crystal Properties Matthews coefficient Solvent content 3.35 63.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.741 α = 109.45 b = 140.568 β = 106.1 c = 157.606 γ = 101.09
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 A DOUBLY FOCUSING TOROIDAL MIRROR M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X26C NSLS X26C
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 3.4 50 93.9 0.15 7.8 3.5 83695
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 3.4 3.52 69 0.44 1.9 2.7
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1JRO 3.4 50 83695 4451 93.7 0.223 0.221 0.2249 0.27 0.278 RANDOM 43.12
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] 0.42 0.25 -4.1 -0.96 -2.4 -3.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.15 r_dihedral_angle_3_deg 19.007 r_dihedral_angle_4_deg 17.291 r_dihedral_angle_1_deg 5.277 r_angle_refined_deg 1.082 r_scangle_it 0.572 r_scbond_it 0.327 r_mcangle_it 0.184 r_mcbond_it 0.095 r_chiral_restr 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.15 r_dihedral_angle_3_deg 19.007 r_dihedral_angle_4_deg 17.291 r_dihedral_angle_1_deg 5.277 r_angle_refined_deg 1.082 r_scangle_it 0.572 r_scbond_it 0.327 r_mcangle_it 0.184 r_mcbond_it 0.095 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_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 36364 Nucleic Acid Atoms Solvent Atoms 43 Heterogen Atoms 400
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing