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The X-ray crystallographic structure of the angiogenesis inhibitor, angiostatin, bound to a peptide from the group A streptococcus protein PAM
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DOH PDB ID 2DOH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 20% PEG 8000, 0.1M potassium phophate (dihydrate), 5% dioxane, soaked in 5mM Pt(C5H5N)2Cl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.16 61.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.467 α = 90 b = 58.467 β = 90 c = 389.146 γ = 120
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 2003-07-15 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 5ID-B 1.0719 APS 5ID-B
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 85.1 0.086 11.5 15828 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 2.8 2.9 22.2 0.507 410
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 ID 2DOH 3.1 20 13107 675 97.01 0.206 0.202 0.202 0.2032 0.296 0.2477 RANDOM 35.457
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] 1.78 0.89 1.78 -2.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.818 r_scangle_it 32.957 r_scbond_it 30.591 r_dihedral_angle_3_deg 25.161 r_dihedral_angle_4_deg 23.7 r_mcangle_it 19.526 r_mcbond_it 15.827 r_dihedral_angle_1_deg 9.614 r_angle_refined_deg 2.593 r_symmetry_hbond_refined 0.457
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.818 r_scangle_it 32.957 r_scbond_it 30.591 r_dihedral_angle_3_deg 25.161 r_dihedral_angle_4_deg 23.7 r_mcangle_it 19.526 r_mcbond_it 15.827 r_dihedral_angle_1_deg 9.614 r_angle_refined_deg 2.593 r_symmetry_hbond_refined 0.457 r_nbd_refined 0.38 r_nbtor_refined 0.372 r_symmetry_vdw_refined 0.358 r_xyhbond_nbd_refined 0.335 r_chiral_restr 0.155 r_bond_refined_d 0.023 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3064 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction