☰ Navigation Tabs
X-ray structure of lfa-1 i-domain in complex with ibe-667 at 1.8a resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XDG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.6 293 0.085M sodium acetate, pH4.6, 0.17M ammonium acetate, 15% glycerol and 25.5% (w/v) PEG4000 , VAPOR DIFFUSION, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.33 47.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.3 α = 90 b = 65.9 β = 90 c = 133.6 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 IMAGE PLATE MAR scanner 345 mm plate 2000-09-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM1A 0.873 ESRF BM1A
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 1.8 8 99 0.072 22.9 4.3 18740 18688
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 1.8 1.86 99 0.134 10.6 4.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1XDG 1.8 7.97 17770 17608 961 99.09 0.17295 0.17295 0.17155 0.1701 0.19934 0.1948 RANDOM 15.01
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] 0.03 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.69 r_dihedral_angle_4_deg 17.097 r_dihedral_angle_3_deg 11.554 r_dihedral_angle_1_deg 5.564 r_scangle_it 2.097 r_scbond_it 1.211 r_angle_refined_deg 0.973 r_mcangle_it 0.684 r_mcbond_it 0.341 r_chiral_restr 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.69 r_dihedral_angle_4_deg 17.097 r_dihedral_angle_3_deg 11.554 r_dihedral_angle_1_deg 5.564 r_scangle_it 2.097 r_scbond_it 1.211 r_angle_refined_deg 0.973 r_mcangle_it 0.684 r_mcbond_it 0.341 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1468 Nucleic Acid Atoms Solvent Atoms 299 Heterogen Atoms 33
Software Software Software Name Purpose MAR345dtb data collection X-PLOR model building REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling X-PLOR phasing