☰ Navigation Tabs
Crystal Structure of Macrophage Migration Inhibitory Factor from Plasmodium falciparum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WKB PDB ENTRY 2WKB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 10% PEG 1000, 10% PEG 8000, 0.2 M KSCN, 0.1 M TRIS-HCL PH 8.0
Crystal Properties Matthews coefficient Solvent content 1.85 33.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.291 α = 90 b = 83.291 β = 90 c = 83.291 γ = 90
Symmetry Space Group P 21 3
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD ADSC QUANTUM 4 MIRRORS 2006-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 2.05 50 99.9 0.04 34.6 14.2 12419 5
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 2.05 2.09 100 0.39 6.1 12.1
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 2WKB 2.05 58.9 11459 587 97.07 0.253 0.24943 0.2566 0.32057 0.3183 RANDOM 32.002
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 r_dihedral_angle_2_deg 40.163 r_dihedral_angle_3_deg 16.068 r_dihedral_angle_4_deg 14.906 r_dihedral_angle_1_deg 6.487 r_scangle_it 4.726 r_scbond_it 3.007 r_mcangle_it 1.865 r_angle_refined_deg 1.815 r_mcbond_it 1.054 r_chiral_restr 0.125
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.163 r_dihedral_angle_3_deg 16.068 r_dihedral_angle_4_deg 14.906 r_dihedral_angle_1_deg 6.487 r_scangle_it 4.726 r_scbond_it 3.007 r_mcangle_it 1.865 r_angle_refined_deg 1.815 r_mcbond_it 1.054 r_chiral_restr 0.125 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 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_mcangle_other r_scbond_other 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 1570 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing