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Macrophage migration inhibitory factor S61H/Y100H mutant (MIF(S61H/Y100H))
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 2.0M ammonium sulfate, 20mM Tris-HCl buffer (pH 7.5), 3% isopropanol
Crystal Properties Matthews coefficient Solvent content 2.66 53.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.789 α = 90 b = 67.932 β = 90 c = 86.771 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 EIGER X 16M 2021-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.0 SPring-8 BL45XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.08 48.031 100 0.062 0.999 18.9 11.4 171618
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.08 1.1 0.684 0.9 3.5
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.08 47.985 171519 8439 99.998 0.139 0.1381 0.1378 0.1549 0.1555 14.173
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] -0.017 0.027 -0.01
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 21.421 r_lrange_other 20.392 r_dihedral_angle_6_deg 15.955 r_dihedral_angle_3_deg 10.406 r_scangle_it 9.692 r_scangle_other 9.689 r_scbond_it 7.67 r_scbond_other 7.668 r_mcbond_it 7.204 r_mcbond_other 7.203
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 21.421 r_lrange_other 20.392 r_dihedral_angle_6_deg 15.955 r_dihedral_angle_3_deg 10.406 r_scangle_it 9.692 r_scangle_other 9.689 r_scbond_it 7.67 r_scbond_other 7.668 r_mcbond_it 7.204 r_mcbond_other 7.203 r_dihedral_angle_2_deg 6.611 r_mcangle_it 6.13 r_mcangle_other 6.128 r_dihedral_angle_1_deg 5.965 r_rigid_bond_restr 4.84 r_angle_refined_deg 1.826 r_angle_other_deg 0.65 r_symmetry_xyhbond_nbd_refined 0.399 r_xyhbond_nbd_refined 0.257 r_nbd_refined 0.24 r_nbd_other 0.211 r_symmetry_nbd_other 0.197 r_nbtor_refined 0.176 r_chiral_restr 0.108 r_symmetry_nbd_refined 0.093 r_symmetry_nbtor_other 0.086 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2607 Nucleic Acid Atoms Solvent Atoms 527 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing