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Crystal structure of the antithrombin-factor IXa-pentasaccharide complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E03 1E03, 1RFN experimental model PDB 1RFN 1E03, 1RFN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 295 0.25M Ammonium sulfate, 19.5% PEG 3350, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.14 60.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.78 α = 90 b = 88.44 β = 90 c = 147.23 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 100 CCD ADSC QUANTUM 315 2009-05-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9796 Diamond I02
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 1.7 58.83 99.3 0.069 0.069 5.7 5.2 113381 112588 26.7
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) 1.7 1.79 100 0.58 0.58 2.2 3.6 16392
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 1E03, 1RFN 1.7 38.05 112588 112546 5670 98.9 0.208 0.208 0.208 0.2259 0.23 0.2236 RANDOM 33.3
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] 0.52 -0.83 0.3
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.1 c_scangle_it 2.94 c_mcangle_it 2.09 c_scbond_it 1.9 c_angle_deg 1.3 c_mcbond_it 1.29 c_improper_angle_d 0.79 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5798 Nucleic Acid Atoms Solvent Atoms 667 Heterogen Atoms 204
Software Software Software Name Purpose PHASER phasing CNS refinement MOSFLM data reduction SCALA data scaling