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CRYSTAL STRUCTURE OF HUMAN GLYCOLATE OXIDASE IN COMPLEX WITH THE INHIBITOR 5-[(4-CHLOROPHENYL)SULFANYL]- 1,2,3-THIADIAZOLE-4-CARBOXYLATE.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NZL PDB ENTRY 2NZL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 CRYSTALLISATION WAS PERFORMED BY THE HANGING DROP VAPOR DIFFUSION METHOD, USING A PRECIPITANT SOLUTION CONTAINING 200 MM NACL, 100 MM MMT AT PH 7.5, AND 15% (W/V) POLYETHYLENE GLYCOL 1000
Crystal Properties Matthews coefficient Solvent content 3.07 59.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.69 α = 90 b = 138.69 β = 90 c = 186.84 γ = 90
Symmetry Space Group P 4 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD ADSC CCD 2007-08-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 ESRF ID14-3
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 2.8 47.4 100 0.09 7 43574 2
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 2NZL 2.84 46.73 41393 2179 100 0.207 0.205 0.1955 0.25 0.237 RANDOM 38.1
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] -0.18 -0.18 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.126 r_dihedral_angle_3_deg 17.131 r_dihedral_angle_4_deg 16.628 r_dihedral_angle_1_deg 5.639 r_scangle_it 1.744 r_angle_refined_deg 1.182 r_scbond_it 1.109 r_mcangle_it 0.844 r_mcbond_it 0.652 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.126 r_dihedral_angle_3_deg 17.131 r_dihedral_angle_4_deg 16.628 r_dihedral_angle_1_deg 5.639 r_scangle_it 1.744 r_angle_refined_deg 1.182 r_scbond_it 1.109 r_mcangle_it 0.844 r_mcbond_it 0.652 r_nbtor_refined 0.302 r_nbd_refined 0.195 r_symmetry_vdw_refined 0.164 r_xyhbond_nbd_refined 0.126 r_symmetry_hbond_refined 0.111 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 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_refined 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_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 10344 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms 188
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing