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Crystal structure of G107A mutant of human macrophage migration inhibitory factor
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 3.71 66.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.863 α = 90 b = 95.863 β = 90 c = 103.712 γ = 120
Symmetry Space Group P 31 2 1
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 2017-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.54 50 83.7 0.082 0.099 0.054 8.2 2.6 15576
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 2.55 2.59 83 0.384 0.476 0.274 0.812 2.4
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 3DJH 2.54 47.93 14698 758 83.01 0.1998 0.1984 0.2084 0.2254 0.2299 RANDOM 35.66
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] -0.01 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.547 r_dihedral_angle_4_deg 25.502 r_dihedral_angle_3_deg 12.459 r_dihedral_angle_1_deg 6.225 r_angle_refined_deg 1.684 r_angle_other_deg 1.072 r_chiral_restr 0.092 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.547 r_dihedral_angle_4_deg 25.502 r_dihedral_angle_3_deg 12.459 r_dihedral_angle_1_deg 6.225 r_angle_refined_deg 1.684 r_angle_other_deg 1.072 r_chiral_restr 0.092 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2548 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 44
Software Software Software Name Purpose HKL-2000 data scaling PHASER phasing REFMAC refinement HKL-2000 data reduction