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Crystal Structure of macrophage migration inhibitory factor (MIF) from Trichomonas vaginalis (I41 form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3T5S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 Morpheus B12: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Tris/BICINE, pH 8.5, 30 mM NaF, 30 mM NaBr and 30 mM NaI. TrvaA.00834.a.UX1.PW39224 at 35.4 mg/mL. 5 mM sodium pyruvate added to the protien prior to crystallization. Plate: 13618 well B12 drop 2, Puck: PSL-0111, Cryo: Direct
Crystal Properties Matthews coefficient Solvent content 2.1 41.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.39 α = 90 b = 118.39 β = 90 c = 106.656 γ = 90
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 EIGER2 XE 9M 2023-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.9795 NSLS-II 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.9 83.71 100 0.075 0.078 0.021 0.999 16.6 13.6 57827
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 1.9 1.95 100 1.619 1.682 0.454 0.637 13.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.9 83.71 1.34 57681 2990 99.75 0.1939 0.192 0.1972 0.2297 0.2334
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 f_dihedral_angle_d 12.096 f_angle_d 0.909 f_chiral_restr 0.067 f_bond_d 0.011 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4713 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 7
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing