☰ Navigation Tabs
Macrophage migration inhibitory factor Y100H mutant (MIF(Y100H))
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 2.0M ammonium sulfate, 20mM Tris-HCl buffer (pH 7.5), 3% isopropanol
Crystal Properties Matthews coefficient Solvent content 2.7 54.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.917 α = 90 b = 68.172 β = 90 c = 87.315 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 EIGER X 16M 2021-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.0 SPring-8 BL45XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.25 48.161 99.7 0.046 0.999 19.7 8.4 112191
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.25 1.27 0.681 0.845 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.25 48.161 112108 5670 99.676 0.127 0.1254 0.1273 0.1517 0.1532 16.159
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] 0.008 0.023 -0.031
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.276 r_lrange_it 15.97 r_lrange_other 13.123 r_dihedral_angle_3_deg 10.887 r_scangle_it 10.286 r_scangle_other 10.283 r_scbond_it 7.688 r_scbond_other 7.685 r_dihedral_angle_2_deg 6.605 r_dihedral_angle_1_deg 5.764
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.276 r_lrange_it 15.97 r_lrange_other 13.123 r_dihedral_angle_3_deg 10.887 r_scangle_it 10.286 r_scangle_other 10.283 r_scbond_it 7.688 r_scbond_other 7.685 r_dihedral_angle_2_deg 6.605 r_dihedral_angle_1_deg 5.764 r_mcangle_it 4.705 r_mcangle_other 4.704 r_rigid_bond_restr 4.67 r_mcbond_it 3.673 r_mcbond_other 3.668 r_angle_refined_deg 1.858 r_angle_other_deg 0.701 r_xyhbond_nbd_refined 0.234 r_nbd_refined 0.232 r_symmetry_xyhbond_nbd_refined 0.226 r_nbd_other 0.201 r_symmetry_nbd_other 0.194 r_nbtor_refined 0.176 r_symmetry_xyhbond_nbd_other 0.151 r_symmetry_nbd_refined 0.151 r_chiral_restr 0.113 r_symmetry_nbtor_other 0.081 r_chiral_restr_other 0.021 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2595 Nucleic Acid Atoms Solvent Atoms 565 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing