2XIZ

Protein kinase Pim-1 in complex with fragment-3 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
15.50.8 M (NH4)2HPO4, 0.1M SODIUM CITRATE PH 5.5, 0.2 M NACL
Crystal Properties
Matthews coefficientSolvent content
3.2862.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.844α = 90
b = 96.844β = 90
c = 80.715γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2008-02-13MSINGLE 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
12.241.691.60.0626.4820132
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)
12.22.358.60.266.36.5

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 STRUCTURE2.2141.591850498290.590.257970.256410.28641RANDOM39.155
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]
0.760.380.76-1.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.773
r_dihedral_angle_4_deg18.821
r_dihedral_angle_3_deg15.354
r_scangle_it5.673
r_dihedral_angle_1_deg5.534
r_scbond_it4.109
r_mcangle_it2.503
r_mcbond_it1.479
r_angle_refined_deg1.123
r_chiral_restr0.086
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.773
r_dihedral_angle_4_deg18.821
r_dihedral_angle_3_deg15.354
r_scangle_it5.673
r_dihedral_angle_1_deg5.534
r_scbond_it4.109
r_mcangle_it2.503
r_mcbond_it1.479
r_angle_refined_deg1.123
r_chiral_restr0.086
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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 Atoms71
Heterogen Atoms11

Software

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