2XJ0

Protein kinase Pim-1 in complex with fragment-4 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 = 96.239α = 90
b = 96.239β = 90
c = 80.457γ = 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
13.142.193.80.1613.28.77338
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)
13.13.1861.80.522.15.2

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 STRUCTURE3.142.11695136493.950.21850.21610.26276RANDOM49.685
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]
4.092.044.09-6.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.116
r_dihedral_angle_4_deg16.028
r_scangle_it8.699
r_dihedral_angle_3_deg8.245
r_scbond_it5.603
r_mcangle_it4.949
r_mcbond_it2.502
r_angle_refined_deg0.727
r_dihedral_angle_1_deg0.491
r_nbtor_refined0.331
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.116
r_dihedral_angle_4_deg16.028
r_scangle_it8.699
r_dihedral_angle_3_deg8.245
r_scbond_it5.603
r_mcangle_it4.949
r_mcbond_it2.502
r_angle_refined_deg0.727
r_dihedral_angle_1_deg0.491
r_nbtor_refined0.331
r_symmetry_vdw_refined0.309
r_nbd_refined0.274
r_xyhbond_nbd_refined0.128
r_symmetry_hbond_refined0.1
r_chiral_restr0.06
r_gen_planes_refined0.003
r_bond_refined_d0.002
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 Atoms2231
Nucleic Acid Atoms
Solvent Atoms12
Heterogen Atoms12

Software

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