2XIY

Protein kinase Pim-1 in complex with fragment-2 from crystallographic fragment screen


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherIN-HOUSE PIM-1 STRUCTURE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.50.9 M (NH4)2HPO4,0.1 M SODIUM CITRATE PH=5.5 , 0.2M NACL
Crystal Properties
Matthews coefficientSolvent content
3.2862.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.987α = 90
b = 96.987β = 90
c = 80.87γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2008-05-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.2BESSY14.2

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
12.248.6960.0921.28.621175
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)
12.22.2871.30.452.254.8

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 REPLACEMENTTHROUGHOUTIN-HOUSE PIM-1 STRUCTURE2.248.6220074106595.970.17150.169940.20075RANDOM18.238
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]
-0.5-0.25-0.50.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.818
r_dihedral_angle_4_deg17.42
r_dihedral_angle_3_deg14.985
r_scangle_it6.381
r_dihedral_angle_1_deg5.742
r_scbond_it4.709
r_mcangle_it2.815
r_mcbond_it1.904
r_angle_refined_deg1.214
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.818
r_dihedral_angle_4_deg17.42
r_dihedral_angle_3_deg14.985
r_scangle_it6.381
r_dihedral_angle_1_deg5.742
r_scbond_it4.709
r_mcangle_it2.815
r_mcbond_it1.904
r_angle_refined_deg1.214
r_nbtor_refined0.304
r_nbd_refined0.187
r_symmetry_vdw_refined0.151
r_xyhbond_nbd_refined0.142
r_symmetry_hbond_refined0.108
r_chiral_restr0.08
r_bond_refined_d0.01
r_gen_planes_refined0.004
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_refined
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 Atoms2234
Nucleic Acid Atoms
Solvent Atoms132
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing