3D94

Crystal structure of the insulin-like growth factor-1 receptor kinase in complex with PQIP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1P4OPDB entry 1P4O

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.529312% PEG8000, 0.1 M imidazole, pH 7.5 and 0.2 M calcium acetate, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.0860.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 208.182α = 90
b = 208.182β = 90
c = 50.853γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42006-09-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X4A0.97913NSLSX4A

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
12.35097.50.07812.341825117319
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)
2.32.3899.20.3942.23.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1P4O2.335.65182511731993297.460.199970.197980.23621RANDOM33.999
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]
-1.48-0.74-1.482.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.844
r_dihedral_angle_4_deg17.089
r_dihedral_angle_3_deg15.479
r_dihedral_angle_1_deg5.949
r_scangle_it2.604
r_scbond_it1.538
r_angle_refined_deg1.29
r_mcangle_it1.262
r_mcbond_it0.709
r_nbtor_refined0.298
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.844
r_dihedral_angle_4_deg17.089
r_dihedral_angle_3_deg15.479
r_dihedral_angle_1_deg5.949
r_scangle_it2.604
r_scbond_it1.538
r_angle_refined_deg1.29
r_mcangle_it1.262
r_mcbond_it0.709
r_nbtor_refined0.298
r_nbd_refined0.199
r_symmetry_vdw_refined0.173
r_symmetry_hbond_refined0.168
r_xyhbond_nbd_refined0.159
r_chiral_restr0.087
r_metal_ion_refined0.063
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_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 Atoms2323
Nucleic Acid Atoms
Solvent Atoms159
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing