2BZK

CRYSTAL STRUCTURE OF THE HUMAN PIM1 IN COMPLEX WITH AMPPNP AND 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 DROP0.1 M SUCCINATE PHOSPHATE GLYCINE BUFFER PH 6, 30% PEG1K, 0.5% DMSO, SITTING DROP
Crystal Properties
Matthews coefficientSolvent content
3.767

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.889α = 90
b = 97.889β = 90
c = 80.493γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU IMAGE PLATEMIRRORS2005-01-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E

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
12.455099.80.19.437.33162163
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)
12.452.55990.553.286.24

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 1XWS2.45421536981499.80.1910.1890.225RANDOM58.89
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]
2.431.212.43-3.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.334
r_dihedral_angle_4_deg15.238
r_dihedral_angle_3_deg14.729
r_dihedral_angle_1_deg6.281
r_scangle_it2.744
r_scbond_it1.636
r_angle_refined_deg1.451
r_mcangle_it1.056
r_angle_other_deg0.792
r_mcbond_it0.593
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.334
r_dihedral_angle_4_deg15.238
r_dihedral_angle_3_deg14.729
r_dihedral_angle_1_deg6.281
r_scangle_it2.744
r_scbond_it1.636
r_angle_refined_deg1.451
r_mcangle_it1.056
r_angle_other_deg0.792
r_mcbond_it0.593
r_symmetry_vdw_other0.264
r_nbd_refined0.207
r_nbtor_refined0.184
r_nbd_other0.178
r_symmetry_hbond_refined0.171
r_symmetry_vdw_refined0.158
r_xyhbond_nbd_refined0.153
r_nbtor_other0.084
r_chiral_restr0.077
r_bond_refined_d0.013
r_gen_planes_refined0.005
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 Atoms2223
Nucleic Acid Atoms
Solvent Atoms23
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing