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X-ray structure of LFA-1 I-domain in complex with LFA878 at 2.1A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CQP PDB ENTRY 1CQP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 sodium citrate, ammonium acetate, glycerol, PEG4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.2 60.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.9 α = 90 b = 77.4 β = 90 c = 92.3 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 293 IMAGE PLATE MARRESEARCH 1999-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM1A 0.80074 ESRF BM1A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.1 8 98.8 0.067 22.5 4.2 29635 29635
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.17 99.8 0.236 6.5
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 (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 1CQP 2.1 8 28105 28105 1492 98.3 0.19205 0.19096 0.2007 0.21276 0.2237 RANDOM 32.077
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] 0.42 -1.72 1.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.032 r_scangle_it 4.362 r_dihedral_angle_1_deg 3.566 r_scbond_it 2.591 r_mcangle_it 1.922 r_angle_refined_deg 1.375 r_mcbond_it 1.077 r_angle_other_deg 0.783 r_symmetry_vdw_other 0.246 r_nbd_refined 0.207
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.032 r_scangle_it 4.362 r_dihedral_angle_1_deg 3.566 r_scbond_it 2.591 r_mcangle_it 1.922 r_angle_refined_deg 1.375 r_mcbond_it 1.077 r_angle_other_deg 0.783 r_symmetry_vdw_other 0.246 r_nbd_refined 0.207 r_nbd_other 0.204 r_symmetry_vdw_refined 0.19 r_xyhbond_nbd_refined 0.127 r_symmetry_hbond_refined 0.125 r_chiral_restr 0.082 r_metal_ion_refined 0.073 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2936 Nucleic Acid Atoms Solvent Atoms 148 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling X-PLOR phasing