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Human D-Dopachrome tautomerase (D-DT)/ macrophage migration inhibitory factor 2 (MIF2) complexed with the selective inhibitor 4-CPPC
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DPT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.8 293 28% - 34% PEG 4000, 0.1 M sodium citrate tribasic dihydrate, pH 5.8, 0.2 M Ammonium acetate
Crystal Properties Matthews coefficient Solvent content 2.18 43.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.936 α = 90 b = 83.936 β = 90 c = 40.479 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 200K 2018-01-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.4 50 100 0.04 0.042 0.013 33.8 7.9 63056
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.42 100 0.147 0.164 0.071 0.983 5.2
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 1DPT 1.4 41.97 60002 3045 99.89 0.1195 0.1177 0.1223 0.1567 0.1603 RANDOM 15.075
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] 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.262 r_sphericity_free 25.392 r_dihedral_angle_4_deg 21.318 r_dihedral_angle_3_deg 10.532 r_sphericity_bonded 9.751 r_dihedral_angle_1_deg 5.692 r_rigid_bond_restr 5.472 r_angle_refined_deg 2.01 r_angle_other_deg 1.961 r_chiral_restr 0.151
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.262 r_sphericity_free 25.392 r_dihedral_angle_4_deg 21.318 r_dihedral_angle_3_deg 10.532 r_sphericity_bonded 9.751 r_dihedral_angle_1_deg 5.692 r_rigid_bond_restr 5.472 r_angle_refined_deg 2.01 r_angle_other_deg 1.961 r_chiral_restr 0.151 r_bond_refined_d 0.025 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2572 Nucleic Acid Atoms Solvent Atoms 404 Heterogen Atoms 21
Software Software Software Name Purpose HKL-2000 data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction