3WOP

Crystal structure of the DAP BII hexapeptide complex II


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3WOI 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP9.529318% PEG 8000, 20% Glycerol, 2mM ZnCl2, 80mM CHES, 2mM Angiotensin IV, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5251.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.96α = 90
b = 120.96β = 90
c = 219.3γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 2702013-02-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A0.97999Photon FactoryBL-17A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.954098.31106632

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3WOI1.9539.87110663583498.150.189990.187150.24444RANDOM23.468
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]
0.220.22-0.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.898
r_dihedral_angle_3_deg16.678
r_dihedral_angle_4_deg13.739
r_dihedral_angle_1_deg6.444
r_long_range_B_refined5.516
r_long_range_B_other5.383
r_scangle_other3.864
r_mcangle_it2.706
r_mcangle_other2.706
r_scbond_it2.465
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.898
r_dihedral_angle_3_deg16.678
r_dihedral_angle_4_deg13.739
r_dihedral_angle_1_deg6.444
r_long_range_B_refined5.516
r_long_range_B_other5.383
r_scangle_other3.864
r_mcangle_it2.706
r_mcangle_other2.706
r_scbond_it2.465
r_scbond_other2.462
r_angle_refined_deg1.859
r_mcbond_it1.804
r_mcbond_other1.804
r_angle_other_deg0.913
r_chiral_restr0.11
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10820
Nucleic Acid Atoms
Solvent Atoms741
Heterogen Atoms58

Software

Software
Software NamePurpose
ADSCdata collection
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling