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Macrophage Migration Inhibitory Factor (MIF) with Covalently Bound FITC
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3L5V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 Ammonium Sulfate, 0.1M Hepes pH 7.0
Crystal Properties Matthews coefficient Solvent content 1.93 36.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.783 α = 90 b = 70.644 β = 90 c = 89.8 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 6M 2016-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.987 PETRA III, EMBL c/o DESY P14 (MX2)
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 1.41 50 99.4 0.068 13.84 11.3 57778
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 1.41 1.44 0.783
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 3L5V 1.41 14.97 54877 2836 99.32 0.13647 0.13381 0.1372 0.18926 0.1302 RANDOM 15.662
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] -0.11 0.06 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.466 r_sphericity_free 36.219 r_dihedral_angle_4_deg 17.918 r_dihedral_angle_3_deg 12.495 r_sphericity_bonded 8.802 r_dihedral_angle_1_deg 5.582 r_long_range_B_refined 5.143 r_long_range_B_other 4.346 r_rigid_bond_restr 2.759 r_scangle_other 2.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.466 r_sphericity_free 36.219 r_dihedral_angle_4_deg 17.918 r_dihedral_angle_3_deg 12.495 r_sphericity_bonded 8.802 r_dihedral_angle_1_deg 5.582 r_long_range_B_refined 5.143 r_long_range_B_other 4.346 r_rigid_bond_restr 2.759 r_scangle_other 2.317 r_scbond_it 1.968 r_scbond_other 1.967 r_mcangle_it 1.653 r_mcangle_other 1.653 r_angle_refined_deg 1.593 r_mcbond_it 1.358 r_mcbond_other 1.357 r_angle_other_deg 1.281 r_chiral_restr 0.161 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2685 Nucleic Acid Atoms Solvent Atoms 385 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing