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Crystal Structure of Antithrombin in the Pentasaccharide-Bound Intermediate State
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E05 PDB entry 1E05
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 292 PEG 3350, Ammonium Fluoride, Tris, glycerol, 1,8-ANS , pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.91 57.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.679 α = 90 b = 86.76 β = 109.54 c = 96.921 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 4 2002-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.1 1.4880 SRS PX14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.6 24.62 99.99 0.092 0.092 6.9 3.6 33483 33481 60.587
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.74 97.8 0.69 0.571 1.9 3.1 14878
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-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 1E05 2.6 24.43 33464 33464 1666 99.5 0.209 0.2124 0.25 0.2526 R-free set was identical to that of PDB entries 1e03, 1e04 and 1e05
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 c_angle_deg 1.3 c_angle_d 1.3 c_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6368 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 312
Software Software Software Name Purpose Adxv data processing SCALA data scaling MOLREP phasing CNS refinement CCP4 data scaling