2C0O

Src family kinase Hck with bound inhibitor A-770041


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1AD5PDB ENTRY 1AD5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8277HCK (10 MG/ML IN 150 MM NACL, 20 MM TRIS.HCL PH 8.0) WAS MIXED WITH A-770041 [100 MM STOCK SOLUTION IN DMSO) TO GIVE A FINAL A-770041 CONCENTRATION OF 1 MM. HCK/A-770041 WAS THEN MIXED WITH RESERVOIR SOLUTION (12% PEG 6000, 3% 1,5-DIAMINOPENTANE, 20% GLYCEROL, 200 MM CA(OAC)2, 100 MM TRIS.HCL PH 8.0) AND EQUILBRATED AGAINST THE RESERVOIR SOLUTION BY VAPOR DIFFUSION (SITTING DROPS) AT 277 K.
Crystal Properties
Matthews coefficientSolvent content
3.159.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.015α = 90
b = 73.176β = 95.52
c = 180.167γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHOSMIC DUAL MIRRORS2003-05-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEENRAF-NONIUS FR591

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
12.855096.10.099.33.22891874.3
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)
12.852.9578.10.392.52.7

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1AD52.854027348144096.20.2040.20.273RANDOM51.89
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]
6.29-3.19-1.3-5.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.634
r_dihedral_angle_3_deg20.623
r_dihedral_angle_4_deg19.645
r_dihedral_angle_1_deg6.884
r_scangle_it2.524
r_angle_refined_deg1.648
r_scbond_it1.497
r_mcangle_it1.075
r_mcbond_it0.608
r_nbtor_refined0.322
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.634
r_dihedral_angle_3_deg20.623
r_dihedral_angle_4_deg19.645
r_dihedral_angle_1_deg6.884
r_scangle_it2.524
r_angle_refined_deg1.648
r_scbond_it1.497
r_mcangle_it1.075
r_mcbond_it0.608
r_nbtor_refined0.322
r_nbd_refined0.236
r_symmetry_hbond_refined0.204
r_xyhbond_nbd_refined0.178
r_symmetry_vdw_refined0.166
r_metal_ion_refined0.164
r_chiral_restr0.101
r_bond_refined_d0.015
r_gen_planes_refined0.006
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6992
Nucleic Acid Atoms
Solvent Atoms248
Heterogen Atoms94

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing