X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherIN-HOUSE PIM1 STRUCTURE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.2pH 7.2
Crystal Properties
Matthews coefficientSolvent content
3.963

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.872α = 90
b = 96.872β = 90
c = 80.844γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray155CCDMARMOSAIC 325 mm CCD2006-11-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-2SSRLBL9-2

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
12.5948.4599.60.1483.9613533-344.9
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)
12.59399.90.7825.1

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 PIM1 STRUCTURE2.5948.451282866899.730.194690.191630.25554RANDOM34.186
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]
0.030.020.03-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.156
r_dihedral_angle_4_deg20.502
r_dihedral_angle_3_deg18.944
r_dihedral_angle_1_deg6.86
r_scangle_it2.805
r_scbond_it1.899
r_angle_refined_deg1.776
r_angle_other_deg1.62
r_mcangle_it1.44
r_mcbond_it1.207
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.156
r_dihedral_angle_4_deg20.502
r_dihedral_angle_3_deg18.944
r_dihedral_angle_1_deg6.86
r_scangle_it2.805
r_scbond_it1.899
r_angle_refined_deg1.776
r_angle_other_deg1.62
r_mcangle_it1.44
r_mcbond_it1.207
r_symmetry_vdw_other0.258
r_nbd_refined0.243
r_nbd_other0.218
r_symmetry_hbond_refined0.205
r_nbtor_refined0.202
r_xyhbond_nbd_refined0.173
r_symmetry_vdw_refined0.166
r_chiral_restr0.162
r_mcbond_other0.157
r_nbtor_other0.105
r_bond_refined_d0.018
r_xyhbond_nbd_other0.017
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_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 Atoms2230
Nucleic Acid Atoms
Solvent Atoms72
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing