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Crystal structure of Pro1 deletion 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 7.5 291 2 M ammonium Sulphate, 3% 2-propanol, 20 mM Tris.HCl, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.74 55.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.096 α = 90 b = 68.155 β = 90 c = 86.902 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 IMAGE PLATE RIGAKU RAXIS IV++ 2015-01-09 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 1.77 50 99.9 0.042 20.7 13.7 40049
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 1.77 1.8 99.7 0.286 12.5
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 1.77 48.17 38016 1969 99.8 0.165 0.164 0.1774 0.188 0.1964 RANDOM 18.52
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 42.873 r_dihedral_angle_4_deg 20.699 r_dihedral_angle_3_deg 12.26 r_dihedral_angle_1_deg 5.484 r_angle_refined_deg 2.137 r_mcangle_it 2.134 r_angle_other_deg 2.122 r_mcbond_it 1.605 r_mcbond_other 1.603 r_chiral_restr 0.127
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.873 r_dihedral_angle_4_deg 20.699 r_dihedral_angle_3_deg 12.26 r_dihedral_angle_1_deg 5.484 r_angle_refined_deg 2.137 r_mcangle_it 2.134 r_angle_other_deg 2.122 r_mcbond_it 1.605 r_mcbond_other 1.603 r_chiral_restr 0.127 r_bond_refined_d 0.023 r_gen_planes_refined 0.013 r_bond_other_d 0.008 r_gen_planes_other 0.006 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2519 Nucleic Acid Atoms Solvent Atoms 254 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction PDB_EXTRACT data extraction HKL-2000 data scaling PHASER phasing