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The X-ray crystallographic structure of the angiogenesis inhibitor, angiostatin, bound a to a peptide from the group A streptococcal surface protein PAM
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KI0 PDB entry 1KI0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 20% PEG 8000, 0.1M potassium phosphate (dihydrate), 5% dioxane, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.16 61.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.377 α = 90 b = 58.377 β = 90 c = 391.033 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD MAR CCD 165 mm 2000-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-ID
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 50 80.2 0.091 12.4 22779 -3
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 2.07 19.1 0.834 524
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-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 1KI0 2.3 15 17617 1775 93.82 0.215 0.21 0.21 0.2154 0.26 0.2594 RANDOM 24.651
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] 1.57 0.79 1.57 -2.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.187 r_scangle_it 4.74 r_scbond_it 3.516 r_mcangle_it 2.279 r_angle_other_deg 1.557 r_angle_refined_deg 1.474 r_mcbond_it 1.405 r_symmetry_hbond_refined 0.428 r_symmetry_vdw_other 0.344 r_xyhbond_nbd_refined 0.337
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.187 r_scangle_it 4.74 r_scbond_it 3.516 r_mcangle_it 2.279 r_angle_other_deg 1.557 r_angle_refined_deg 1.474 r_mcbond_it 1.405 r_symmetry_hbond_refined 0.428 r_symmetry_vdw_other 0.344 r_xyhbond_nbd_refined 0.337 r_nbd_other 0.276 r_nbd_refined 0.261 r_symmetry_vdw_refined 0.198 r_nbtor_other 0.099 r_chiral_restr 0.079 r_bond_refined_d 0.014 r_bond_other_d 0.005 r_gen_planes_refined 0.005 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1521 Nucleic Acid Atoms Solvent Atoms 311 Heterogen Atoms 6
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction