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Crystal structure of the exosite-containing fragment of human ADAMTS13 (P475S mutant)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GHM PDB ENTRY 3GHM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 20% PEG1500, 0.1M MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.21 61.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.378 α = 90 b = 53.243 β = 111.56 c = 76.615 γ = 90
Symmetry Space Group C 1 2 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 315 2011-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0 SPring-8 BL38B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 50 99.1 0.048 20.3 3.7 14407 14278
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9 99 0.31 6.28 3.7 1405
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 PDB ENTRY 3GHM 2.8 30.93 13674 13509 738 98.79 0.232 0.232 0.229 0.2297 0.277 0.2288 RANDOM 62.369
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] -2.99 -3.66 2.48 -2.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.703 r_dihedral_angle_4_deg 14.882 r_dihedral_angle_3_deg 13.985 r_dihedral_angle_1_deg 5.237 r_scangle_it 1.691 r_angle_refined_deg 0.95 r_scbond_it 0.95 r_angle_other_deg 0.736 r_mcangle_it 0.666 r_mcbond_it 0.348
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.703 r_dihedral_angle_4_deg 14.882 r_dihedral_angle_3_deg 13.985 r_dihedral_angle_1_deg 5.237 r_scangle_it 1.691 r_angle_refined_deg 0.95 r_scbond_it 0.95 r_angle_other_deg 0.736 r_mcangle_it 0.666 r_mcbond_it 0.348 r_chiral_restr 0.055 r_mcbond_other 0.033 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2894 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms 74
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling