2C3I

CRYSTAL STRUCTURE OF HUMAN PIM1 IN COMPLEX WITH IMIDAZOPYRIDAZIN I


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystal Properties
Matthews coefficientSolvent content
3.767

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.439α = 90
b = 98.439β = 90
c = 80.843γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2005-09-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SASLSX10SA

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
11.936.597.20.082.393.5340632
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)
11.92920.592.392.6

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 1XWS1.985.1332279170997.10.1870.1850.219RANDOM29.7
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]
0.720.360.72-1.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.093
r_dihedral_angle_4_deg15.599
r_dihedral_angle_3_deg13.219
r_dihedral_angle_1_deg9.915
r_scangle_it4.147
r_scbond_it2.653
r_mcangle_it1.952
r_angle_refined_deg1.599
r_mcbond_it1.253
r_angle_other_deg0.895
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.093
r_dihedral_angle_4_deg15.599
r_dihedral_angle_3_deg13.219
r_dihedral_angle_1_deg9.915
r_scangle_it4.147
r_scbond_it2.653
r_mcangle_it1.952
r_angle_refined_deg1.599
r_mcbond_it1.253
r_angle_other_deg0.895
r_symmetry_hbond_refined0.32
r_xyhbond_nbd_refined0.293
r_symmetry_vdw_other0.292
r_nbd_refined0.207
r_nbtor_refined0.186
r_nbd_other0.182
r_chiral_restr0.103
r_nbtor_other0.085
r_symmetry_vdw_refined0.061
r_bond_refined_d0.018
r_gen_planes_refined0.007
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 Atoms2209
Nucleic Acid Atoms
Solvent Atoms157
Heterogen Atoms23

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing