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Structure of dimeric antithrombin complexed with a P14-P9 reactive loop peptide and an exogenous tripeptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JVQ Dimeric antithrombin complexed with a P14-P8 reactive loop peptide and an exogenous tetrapeptide (1jvq). Both peptides omitted in starting model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 298 PEG 4000, sodium cacodylate, ammonium fluoride, glycerol, pH 6.8,
VAPOR DIFFUSION, HANGING DROP at 298K
Crystal Properties Matthews coefficient Solvent content 3.07 59.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.811 α = 90 b = 99.908 β = 104.44 c = 87.292 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 2002-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.2 0.978 SRS PX14.2
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 2.8 37.58 96.7 0.104 0.087 7.5 3.3 27398 27376 -3.7 51.2
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 2.8 2.95 81.5 0.551 0.431 1.7 2.5 3351
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 Dimeric antithrombin complexed with a P14-P8 reactive loop peptide
and an exogenous tetrapeptide (1jvq). Both peptides omitted in starting model 2.8 34.03 28306 27351 1374 96.6 0.202 0.1944 0.266 0.2615 Random 55.26
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] -0.54 -5.53 9.09 -8.56
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23 c_angle_deg 1.3 c_improper_angle_d 0.81 c_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6603 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms 126
Software Software Software Name Purpose MOSFLM data reduction TRUNCATE data reduction CNS refinement CCP4 data scaling CNS phasing