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Structure of macrophage migration inhibitory factor (MIF) with caffeic acid at 1.9A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CA7 PDB entry 1CA7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 296 30-42.5% MPD_P1K_P3350 mix (MDL Morpheus screen), 0.1M buffer 1 mix (MDL morpheus screen), pH 5.5-7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 2.52 51.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.669 α = 90 b = 67.988 β = 90 c = 89.135 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 CCD ADSC QUANTUM 315 double Si 111 crystal monochromator 2009-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9702 Diamond I04
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 37.3 99.3 0.109 8.4 4.43 32859 24.8
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 1.97 100 0.254 4.1 4.53
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 PDB entry 1CA7 1.9 32.27 31196 1663 99.3 0.17422 0.17283 0.188 0.19958 0.2083 RANDOM 16.023
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] -0.21 -0.59 0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.157 r_dihedral_angle_3_deg 13.895 r_dihedral_angle_4_deg 13.417 r_dihedral_angle_1_deg 5.636 r_scangle_it 3.835 r_scbond_it 2.419 r_angle_refined_deg 1.408 r_mcangle_it 1.279 r_mcbond_it 0.726 r_chiral_restr 0.116
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.157 r_dihedral_angle_3_deg 13.895 r_dihedral_angle_4_deg 13.417 r_dihedral_angle_1_deg 5.636 r_scangle_it 3.835 r_scbond_it 2.419 r_angle_refined_deg 1.408 r_mcangle_it 1.279 r_mcbond_it 0.726 r_chiral_restr 0.116 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2662 Nucleic Acid Atoms Solvent Atoms 272 Heterogen Atoms 13
Software Software Software Name Purpose DNA data collection PHASER phasing REFMAC refinement CrystalClear data reduction CrystalClear data scaling