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HUMAN MACROPHAGE MIGRATION INHIBITORY FACTOR (MIF)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MIF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 298 ammonium sulfate, sodium citrate, pH 5.0, vapor diffusion : hanging drop, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.5 50.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.5 α = 90 b = 67.5 β = 90 c = 88.3 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 DIFFRACTOMETER WEISSENBERG 1998-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6B Photon Factory BL-6B
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 1.5 100 86.9 0.026 18.7 2.7 56679 56679 21.9
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) 1.5 1.54 67.1 0.359 1.95 5037
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1MIF 1.5 100 2 50908 5771 86.9 0.191 0.191 0.1871 0.214 0.2136 RANDOM 18.6
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 x_dihedral_angle_d 26.1 x_scangle_it 4.73 x_scbond_it 3.07 x_mcangle_it 1.88 x_angle_deg 1.5 x_mcbond_it 1.4 x_improper_angle_d 0.87 x_bond_d 0.013 x_bond_d_na x_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 26.1 x_scangle_it 4.73 x_scbond_it 3.07 x_mcangle_it 1.88 x_angle_deg 1.5 x_mcbond_it 1.4 x_improper_angle_d 0.87 x_bond_d 0.013 x_bond_d_na x_bond_d_prot x_angle_d x_angle_d_na x_angle_d_prot x_angle_deg_na x_angle_deg_prot x_dihedral_angle_d_na x_dihedral_angle_d_prot x_improper_angle_d_na x_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2672 Nucleic Acid Atoms Solvent Atoms 334 Heterogen Atoms 74
Software Software Software Name Purpose X-PLOR model building X-PLOR refinement DENZO data reduction CCP4 data scaling X-PLOR phasing