4MBI

Discovery of Pyrazolo[1,5a]pyrimidine-based Pim1 Inhibitors


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.429810.5% PEG 400, 0.05 M Tris-Cl pH 8.4, 0.3 M NaCl, 0.01 M DTT, 0.01M EDTA, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.2962.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.877α = 90
b = 97.877β = 90
c = 80.625γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200IMAGE PLATERIGAKU RAXIS IV++MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.329.880.92134017271

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT2.329.771571515715176989.250.214840.211250.24564RANDOM30.024
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]
0.90.450.9-1.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.61
r_dihedral_angle_4_deg20.728
r_dihedral_angle_3_deg16.202
r_dihedral_angle_1_deg6.856
r_scangle_it3.128
r_scbond_it2.02
r_angle_refined_deg1.705
r_mcangle_it1.251
r_angle_other_deg0.96
r_mcbond_it0.687
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.61
r_dihedral_angle_4_deg20.728
r_dihedral_angle_3_deg16.202
r_dihedral_angle_1_deg6.856
r_scangle_it3.128
r_scbond_it2.02
r_angle_refined_deg1.705
r_mcangle_it1.251
r_angle_other_deg0.96
r_mcbond_it0.687
r_mcbond_other0.15
r_chiral_restr0.094
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
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_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 Atoms124
Heterogen Atoms20

Software

Software
Software NamePurpose
CrystalCleardata collection
AMoREphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling