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Crystal Structure of macrophage migration inhibitory factor (MIF) from Trichomonas vaginalis (Apo, P41212 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 Berkeley D5: 100 mM Hepes free acid/ Sodium hydroxide pH 7.5 200 mM Ammonium acetate 25% (w/v) PEG 3350. TrvaA.00834.a.UX1.PW39224 at 35.4 mg/mL. Plate: 13617 well D5 drop 2, Puck: PSL-1907, Cryo: 20% PEG 200 + 80% crystallant
Crystal Properties Matthews coefficient Solvent content 2.22 44.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.715 α = 90 b = 80.715 β = 90 c = 121.152 γ = 90
Symmetry Space Group P 41 21 2
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 2023-10-09 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 2.4 80.71 100 0.091 0.093 0.02 0.999 21.2 23.2 16349
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 2.4 2.46 100 2.689 2.745 0.549 0.627 24.6
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.4 67.17 1.35 16289 816 99.96 0.2463 0.2453 0.2642 0.2612
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 4.594 f_angle_d 1.124 f_chiral_restr 0.07 f_plane_restr 0.012 f_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2588 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing