2DOH

The X-ray crystallographic structure of the angiogenesis inhibitor, angiostatin, bound a to a peptide from the group A streptococcal surface protein PAM


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1KI0PDB entry 1KI0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29820% PEG 8000, 0.1M potassium phosphate (dihydrate), 5% dioxane, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.1661.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.377α = 90
b = 58.377β = 90
c = 391.033γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDMAR CCD 165 mm2000-03-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.0APS17-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
125080.20.09112.422779-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0719.10.834524

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1KI02.31517617177593.820.2150.210.210.26RANDOM24.651
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]
1.570.791.57-2.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.187
r_scangle_it4.74
r_scbond_it3.516
r_mcangle_it2.279
r_angle_other_deg1.557
r_angle_refined_deg1.474
r_mcbond_it1.405
r_symmetry_hbond_refined0.428
r_symmetry_vdw_other0.344
r_xyhbond_nbd_refined0.337
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.187
r_scangle_it4.74
r_scbond_it3.516
r_mcangle_it2.279
r_angle_other_deg1.557
r_angle_refined_deg1.474
r_mcbond_it1.405
r_symmetry_hbond_refined0.428
r_symmetry_vdw_other0.344
r_xyhbond_nbd_refined0.337
r_nbd_other0.276
r_nbd_refined0.261
r_symmetry_vdw_refined0.198
r_nbtor_other0.099
r_chiral_restr0.079
r_bond_refined_d0.014
r_bond_other_d0.005
r_gen_planes_refined0.005
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1521
Nucleic Acid Atoms
Solvent Atoms311
Heterogen Atoms6

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction