☰ Navigation Tabs
Mapping the binding trajectory of a suicide inhibitor in human indoleamine 2,3-dioxygenase 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5WMU PDB entry 5WMU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 10 277 100 mM sodium thiosulfate, 100 mM CAPS, pH 10.0, 200 mM sodium chloride, 20% w/v PEG8000
Crystal Properties Matthews coefficient Solvent content 3.01 59.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.534 α = 90 b = 97.234 β = 90 c = 128.289 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 RAYONIX MX225HE 2017-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97931 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 3.2 29.5 99.9 0.25 0.101 0.992 6.7 7.1 18253
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.37 100 1.465 0.588 0.508 1.3 7.2
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 5WMU 3.2 29.5 17304 906 99.82 0.19876 0.19649 0.2042 0.24151 0.2467 RANDOM 85.609
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] -4.92 -2.62 7.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.074 r_dihedral_angle_4_deg 21.481 r_dihedral_angle_3_deg 20.222 r_long_range_B_refined 13.744 r_long_range_B_other 13.743 r_mcangle_other 10.196 r_mcangle_it 10.194 r_scangle_other 9.638 r_dihedral_angle_1_deg 9.224 r_mcbond_it 6.506
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.074 r_dihedral_angle_4_deg 21.481 r_dihedral_angle_3_deg 20.222 r_long_range_B_refined 13.744 r_long_range_B_other 13.743 r_mcangle_other 10.196 r_mcangle_it 10.194 r_scangle_other 9.638 r_dihedral_angle_1_deg 9.224 r_mcbond_it 6.506 r_mcbond_other 6.505 r_scbond_it 5.895 r_scbond_other 5.895 r_angle_other_deg 0.729 r_angle_refined_deg 0.668 r_chiral_restr 0.036 r_gen_planes_refined 0.009 r_gen_planes_other 0.004 r_bond_refined_d 0.002 r_bond_other_d 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5787 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms 125
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing