☰ Navigation Tabs
Crystal structure of N110A 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 293 2 M ammonium sulfate, 3 % 2-propanol, 0.1 M Tris-HCl, pH 7.0 - 8.0
Crystal Properties Matthews coefficient Solvent content 2.73 54.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.918 α = 90 b = 68.253 β = 90 c = 86.898 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 2017-01-25 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 1.68 50 97.5 0.06 0.067 0.029 11 3.8 45605
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 1.68 1.71 92.7 0.303 0.371 0.21 0.707 2.6
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 1.68 48.14 43122 2291 97.14 0.1528 0.1516 0.1556 0.1753 0.1778 RANDOM 15.322
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 r_dihedral_angle_2_deg 42.219 r_dihedral_angle_4_deg 21.351 r_dihedral_angle_3_deg 11.57 r_dihedral_angle_1_deg 5.442 r_angle_other_deg 3.062 r_angle_refined_deg 2.005 r_chiral_restr 0.156 r_bond_refined_d 0.022 r_gen_planes_refined 0.01 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.219 r_dihedral_angle_4_deg 21.351 r_dihedral_angle_3_deg 11.57 r_dihedral_angle_1_deg 5.442 r_angle_other_deg 3.062 r_angle_refined_deg 2.005 r_chiral_restr 0.156 r_bond_refined_d 0.022 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2556 Nucleic Acid Atoms Solvent Atoms 307 Heterogen Atoms 46
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling PHASER model building REFMAC refinement PDB_EXTRACT data extraction PHASER phasing