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Neutron crystal structure of human macrophage migration inhibitory factor
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7XTX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 283 0.49 M Monosodium phosphate, 0.91 M Dipotassium phosphate
Crystal Properties Matthews coefficient Solvent content 3.83 67.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.534 α = 90 b = 96.534 β = 90 c = 105.596 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 neutron 293 DIFFRACTOMETER iBIX The used detector is described in the paper (https://iopscience.iop.org/article/10.1088/1742-6596/528/1/012042/pdf). 2020-06-24 L LAUE 2 1 x-ray 293 PIXEL DECTRIS PILATUS3 6M 2020-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SPALLATION SOURCE J-PARC MLF BEAMLINE BL-03 3.05-5.47 JPARC MLF BL-03 2 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (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 2 1.6 48.27 99.9 0.996 14.7 10 75394 20.95 1 2 20 99.4 0.984 7.9 6.6 38853
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 1.6 1.63 0.923 1 2 2.11 0.431
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1.6 44.64 1.93 75322 3993 100 0.1547 0.1539 0.1564 0.1692 0.1712 29.16 NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 2 20 38853 99.4 0.18 0.2
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 f_dihedral_angle_d 19.1828 f_angle_d 1.5558 f_chiral_restr 0.113 f_bond_d 0.041 f_plane_restr 0.0074
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2579 Nucleic Acid Atoms Solvent Atoms 215 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement SCALA data scaling MOLREP phasing PDB_EXTRACT data extraction