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Crystal structure of macrophage migration inhibitory factor in complex with T614
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DJH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 2 M ammonium sulfate, 3 % 2-propanol, 0.1 M Tris-HCl, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.74 55.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.677 α = 90 b = 67.944 β = 90 c = 88.371 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 PIXEL DECTRIS PILATUS 200K 2015-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.73 50 99.5 0.054 0.026 16.6 3.9 43220
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 1.73 1.76 98.2 0.118 0.138 0.069 0.976 3.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.73 42.18 40780 2276 99.52 0.1752 0.17369 0.1863 0.20246 0.2105 RANDOM 13.48
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] -0.02 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.537 r_dihedral_angle_4_deg 19.224 r_dihedral_angle_3_deg 11.233 r_dihedral_angle_1_deg 5.536 r_long_range_B_refined 4.788 r_long_range_B_other 4.787 r_scangle_other 3.521 r_angle_other_deg 2.912 r_scbond_it 2.442 r_scbond_other 2.441
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.537 r_dihedral_angle_4_deg 19.224 r_dihedral_angle_3_deg 11.233 r_dihedral_angle_1_deg 5.536 r_long_range_B_refined 4.788 r_long_range_B_other 4.787 r_scangle_other 3.521 r_angle_other_deg 2.912 r_scbond_it 2.442 r_scbond_other 2.441 r_angle_refined_deg 2.371 r_mcangle_other 1.644 r_mcangle_it 1.641 r_mcbond_it 1.205 r_mcbond_other 1.194 r_chiral_restr 0.164 r_bond_other_d 0.035 r_bond_refined_d 0.027 r_gen_planes_other 0.019 r_gen_planes_refined 0.012 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 2551 Nucleic Acid Atoms Solvent Atoms 432 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction PHASER phasing