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X-ray structure of LFA-1 I-domain bound to a 1,4-diazepane-2,5-dione inhibitor at 1.8A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CQP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 PEG 6000, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.4 49.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.259 α = 90 b = 59.995 β = 90 c = 142.616 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 2000-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM1A 0.80000 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 1.8 8 99.7 0.067 29.4 7.8 35097 35097 19.8
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) 1.8 1.86 99.3 0.4 4.3 3631
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 1CQP 1.8 8 35097 35097 1844 99.73 0.18505 0.18353 0.1935 0.21409 0.2245 RANDOM 21.754
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] 0.27 -0.75 0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.889 r_dihedral_angle_4_deg 16.618 r_dihedral_angle_3_deg 13.227 r_dihedral_angle_1_deg 5.734 r_scangle_it 3.12 r_scbond_it 2.21 r_mcangle_it 1.391 r_angle_refined_deg 1.283 r_mcbond_it 1.246 r_angle_other_deg 0.773
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.889 r_dihedral_angle_4_deg 16.618 r_dihedral_angle_3_deg 13.227 r_dihedral_angle_1_deg 5.734 r_scangle_it 3.12 r_scbond_it 2.21 r_mcangle_it 1.391 r_angle_refined_deg 1.283 r_mcbond_it 1.246 r_angle_other_deg 0.773 r_symmetry_vdw_other 0.286 r_nbd_refined 0.205 r_mcbond_other 0.187 r_symmetry_vdw_refined 0.174 r_nbd_other 0.172 r_xyhbond_nbd_refined 0.144 r_symmetry_hbond_refined 0.144 r_nbtor_other 0.086 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2866 Nucleic Acid Atoms Solvent Atoms 246 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling X-PLOR phasing