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Crystal structure of H62F 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 2.72 54.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.084 α = 90 b = 68.263 β = 90 c = 86.966 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 200K 2018-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 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 1.55 50 99.7 0.047 0.05 0.016 18.1 6.9 59338
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 1.55 1.58 98.7 0.225 0.255 0.118 0.953 4.5
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 1.55 48.21 56183 3090 99.65 0.1197 0.1178 0.1201 0.1538 0.1539 RANDOM 14.621
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 0.02 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.91 r_rigid_bond_restr 15.398 r_dihedral_angle_4_deg 15.245 r_dihedral_angle_3_deg 10.366 r_dihedral_angle_1_deg 5.811 r_angle_other_deg 2.73 r_angle_refined_deg 1.751 r_chiral_restr 0.111 r_bond_other_d 0.035 r_gen_planes_other 0.018
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.91 r_rigid_bond_restr 15.398 r_dihedral_angle_4_deg 15.245 r_dihedral_angle_3_deg 10.366 r_dihedral_angle_1_deg 5.811 r_angle_other_deg 2.73 r_angle_refined_deg 1.751 r_chiral_restr 0.111 r_bond_other_d 0.035 r_gen_planes_other 0.018 r_bond_refined_d 0.017 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2594 Nucleic Acid Atoms Solvent Atoms 327 Heterogen Atoms 37
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction