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Crystal structure of Pro1 deletion and M2A double mutant of 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 2.76 55.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.598 α = 90 b = 67.627 β = 90 c = 88.46 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 2014-03-15 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) 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 1.9 23.9 99.7 0.029 42.4 5 32624
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.93 99.9 0.102 4.9 1617
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3DJH 1.9 23.9 32577 1591 99.76 0.1723 0.1714 0.1911 0.2188 RANDOM 20.98
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.925 r_dihedral_angle_4_deg 21.56 r_dihedral_angle_3_deg 10.123 r_dihedral_angle_1_deg 5.808 r_mcangle_it 2.295 r_angle_other_deg 1.876 r_mcbond_it 1.77 r_mcbond_other 1.77 r_angle_refined_deg 1.729 r_chiral_restr 0.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.925 r_dihedral_angle_4_deg 21.56 r_dihedral_angle_3_deg 10.123 r_dihedral_angle_1_deg 5.808 r_mcangle_it 2.295 r_angle_other_deg 1.876 r_mcbond_it 1.77 r_mcbond_other 1.77 r_angle_refined_deg 1.729 r_chiral_restr 0.112 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_bond_other_d 0.008 r_gen_planes_other 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2481 Nucleic Acid Atoms Solvent Atoms 257 Heterogen Atoms 9
Software Software Software Name Purpose DENZO data reduction REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data scaling PHASER phasing SCALEPACK data scaling