2AOA | pdb_00002aoa

Crystal structures of a high-affinity macrocyclic peptide mimetic in complex with the Grb2 SH2 domain


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION5.7298PEG3350, sodium chloride, sodium acetate, pH 5.7, VAPOR DIFFUSION, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.652.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.173α = 90
b = 102.659β = 90
c = 107.24γ = 90
Symmetry
Space GroupF 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDMARRESEARCH2004-06-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1APS22-ID

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
11.9956.89517.9515744137332237.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0791

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.9956.8157441373379994.020.248620.245550.250.30711RANDOM40.738
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]
-0.79-0.221.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg10.265
r_scangle_it6.72
r_scbond_it4.676
r_angle_refined_deg3.755
r_mcangle_it3.397
r_mcbond_it2.071
r_angle_other_deg1.836
r_chiral_restr0.658
r_symmetry_hbond_refined0.465
r_xyhbond_nbd_refined0.347
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg10.265
r_scangle_it6.72
r_scbond_it4.676
r_angle_refined_deg3.755
r_mcangle_it3.397
r_mcbond_it2.071
r_angle_other_deg1.836
r_chiral_restr0.658
r_symmetry_hbond_refined0.465
r_xyhbond_nbd_refined0.347
r_nbd_other0.287
r_nbd_refined0.268
r_symmetry_vdw_other0.249
r_nbtor_other0.128
r_symmetry_vdw_refined0.073
r_bond_refined_d0.044
r_gen_planes_refined0.019
r_gen_planes_other0.013
r_bond_other_d0.003
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1302
Nucleic Acid Atoms
Solvent Atoms103
Heterogen Atoms187

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
SCALEPACKdata scaling
AMoREphasing