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D-dopachrome tautomerase (D-DT)/macrophage migration inhibitory factor 2 (MIF2) complexed with inhibitor 4-IPP
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 8 293.15 0.2 M Sodium chloride, 0.1 M Tris pH 8.5, 25% w/v Polyethylene glycol 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 2.14 42.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.286 α = 90 b = 83.286 β = 90 c = 40.303 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 CCD ADSC QUANTUM 315 2009-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.0 NSLS X25
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 1.13 50 99.89 0.125 20.97 5.1 116532 116400
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) 1.13 1.17 94.2 0.269 4.31 9.1
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 1DPT 1.13 36.06 114070 114070 2329 99.89 0.11208 0.11172 0.1088 0.12927 0.1258 RANDOM 7.087
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.852 r_dihedral_angle_4_deg 17.209 r_dihedral_angle_3_deg 11.169 r_dihedral_angle_1_deg 6.174 r_scangle_it 3.962 r_scbond_it 2.672 r_mcangle_it 1.883 r_angle_refined_deg 1.489 r_mcbond_it 1.201 r_angle_other_deg 0.974
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.852 r_dihedral_angle_4_deg 17.209 r_dihedral_angle_3_deg 11.169 r_dihedral_angle_1_deg 6.174 r_scangle_it 3.962 r_scbond_it 2.672 r_mcangle_it 1.883 r_angle_refined_deg 1.489 r_mcbond_it 1.201 r_angle_other_deg 0.974 r_rigid_bond_restr 0.914 r_mcbond_other 0.322 r_chiral_restr 0.09 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2655 Nucleic Acid Atoms Solvent Atoms 496 Heterogen Atoms 38
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling