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Crystal Structure of Native Heparin Cofactor II
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other several serpins were tried best solution with native antithrombin
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 MgCl2, Tris, PEG 4000, glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP at 298K
Crystal Properties Matthews coefficient Solvent content 2.45 49.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.73 α = 90 b = 80 β = 102.04 c = 92.24 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 mirrors 2000-11-07 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 2.35 30 66 0.14 0.14 4 2.9 40150 2 1 38.39
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 2.35 2.58 72.9 0.45 0.35 1.5 1.6 7595
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 several serpins were tried best solution with native antithrombin 2.35 25 39156 994 88 0.208 0.2087 0.255 0.25 random 37.7
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] 13.95 12.1 -9.52 -4.43
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 3.429 c_scbond_it 2.229 c_mcangle_it 2.182 c_angle_deg 1.3 c_mcbond_it 1.297 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6372 Nucleic Acid Atoms Solvent Atoms 297 Heterogen Atoms 54
Software Software Software Name Purpose MOLREP phasing CNS refinement MOSFLM data reduction CCP4 data scaling