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Crystal structure of N97A 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 54.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.134 α = 90 b = 68.269 β = 90 c = 86.392 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 2017-01-17 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 1.71 50 99.7 0.066 0.072 0.028 8.1 4.7 44201
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 1.71 1.74 99.4 0.199 0.24 0.132 0.946 3
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 1.71 48.23 41899 2166 99.42 0.1567 0.1556 0.1702 0.1785 0.1911 RANDOM 14.798
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.01 r_dihedral_angle_4_deg 19.618 r_dihedral_angle_3_deg 11.261 r_dihedral_angle_1_deg 5.453 r_angle_other_deg 4.879 r_angle_refined_deg 2.023 r_chiral_restr 0.144 r_bond_refined_d 0.026 r_gen_planes_other 0.021 r_gen_planes_refined 0.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.01 r_dihedral_angle_4_deg 19.618 r_dihedral_angle_3_deg 11.261 r_dihedral_angle_1_deg 5.453 r_angle_other_deg 4.879 r_angle_refined_deg 2.023 r_chiral_restr 0.144 r_bond_refined_d 0.026 r_gen_planes_other 0.021 r_gen_planes_refined 0.011 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2558 Nucleic Acid Atoms Solvent Atoms 312 Heterogen Atoms 38
Software Software Software Name Purpose HKL-2000 data scaling PHASER model building REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing HKL data scaling