2BIL

The human protein kinase Pim1 in complex with its consensus peptide Pimtide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1XWSPDB ENTRY 1XWS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2770.1 M MSPG, 30% PEG1K, 0.5% DMSO, SITTING DROP, VAPOR DIFFUSION, 277 K
Crystal Properties
Matthews coefficientSolvent content
3.767

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.1α = 90
b = 98.1β = 90
c = 80.04γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS HTCMULTILAYER MIRRORS2004-12-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU

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
12.5542.48990.139.76.7142592.5
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)
12.552.65970.512.74.1

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 1XWS2.5524.51350171498.90.1950.1920.248RANDOM33.66
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]
1.370.691.37-2.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.736
r_dihedral_angle_4_deg20.114
r_dihedral_angle_3_deg15.567
r_dihedral_angle_1_deg6.188
r_scangle_it2.995
r_angle_refined_deg1.974
r_scbond_it1.791
r_mcangle_it1.236
r_angle_other_deg0.858
r_mcbond_it0.729
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.736
r_dihedral_angle_4_deg20.114
r_dihedral_angle_3_deg15.567
r_dihedral_angle_1_deg6.188
r_scangle_it2.995
r_angle_refined_deg1.974
r_scbond_it1.791
r_mcangle_it1.236
r_angle_other_deg0.858
r_mcbond_it0.729
r_symmetry_vdw_other0.276
r_nbd_refined0.221
r_nbtor_refined0.189
r_nbd_other0.186
r_xyhbond_nbd_refined0.15
r_symmetry_vdw_refined0.117
r_symmetry_hbond_refined0.114
r_chiral_restr0.091
r_nbtor_other0.088
r_bond_refined_d0.017
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
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_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 Atoms2264
Nucleic Acid Atoms
Solvent Atoms48
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing